[ { "id": "authors:jd3th-g0g46", "collection": "authors", "collection_id": "jd3th-g0g46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221212-796622400.30", "type": "article", "title": "Smart data collection for CryoEM", "author": [ { "family_name": "Bepler", "given_name": "Tristan", "orcid": "0000-0001-5595-9954", "clpid": "Bepler-Tristan" }, { "family_name": "Borst", "given_name": "Andrew J.", "orcid": "0000-0003-4297-7824", "clpid": "Borst-Andrew-J" }, { "family_name": "Bouvette", "given_name": "Jonathan", "orcid": "0000-0003-3550-5319", "clpid": "Bouvette-Jonathan" }, { "family_name": "Cannone", "given_name": "Giuseppe", "orcid": "0000-0002-4381-2522", "clpid": "Cannone-Giuseppe" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Cheng", "given_name": "Anchi", "orcid": "0000-0003-0466-4376", "clpid": "Cheng-Anchi" }, { "family_name": "Cheng", "given_name": "Ao", "clpid": "Cheng-Ao" }, { "family_name": "Fan", "given_name": "Quanfu", "clpid": "Fan-Quanfu" }, { "family_name": "Grollios", "given_name": "Fanis", "clpid": "Grollios-Fanis" }, { "family_name": "Gupta", "given_name": "Harshit", "orcid": "0000-0002-2910-9072", "clpid": "Gupta-Harshit" }, { "family_name": "Gupta", "given_name": "Meghna", "orcid": "0000-0002-7432-3211", "clpid": "Gupta-Meghna" }, { "family_name": "Humphreys", "given_name": "Theo", "clpid": "Humphreys-Theo" }, { "family_name": "Kim", "given_name": "Paul T.", "clpid": "Kim-Paul-T" }, { "family_name": "Kuang", "given_name": "Huihui", "orcid": "0000-0002-9891-1747", "clpid": "Kuang-Huihui" }, { "family_name": "Li", "given_name": "Yilai", "clpid": "Li-Yilai" }, { "family_name": "Noble", "given_name": "Alex J.", "orcid": "0000-0001-8634-2279", "clpid": "Noble-Alex-J" }, { "family_name": "Punjani", "given_name": "Ali", "orcid": "0000-0002-4133-6630", "clpid": "Punjani-Ali" }, { "family_name": "Rice", "given_name": "William J.", "orcid": "0000-0002-5187-255X", "clpid": "Rice-William-J" }, { "family_name": "S. Sorzano", "given_name": "Carlos Oscar", "orcid": "0000-0002-9473-283X", "clpid": "S-Sorzano-Carlos-Oscar" }, { "family_name": "Stagg", "given_name": "Scott M.", "orcid": "0000-0001-8855-4152", "clpid": "Stagg-Scott-M" }, { "family_name": "Strauss", "given_name": "Joshua", "orcid": "0000-0002-0393-9887", "clpid": "Strauss-Joshua" }, { "family_name": "Yu", "given_name": "Lingbo", "clpid": "Yu-Lingbo" }, { "family_name": "Carragher", "given_name": "Bridget", "orcid": "0000-0002-0624-5020", "clpid": "Carragher-Bridget" }, { "family_name": "Potter", "given_name": "Clinton S.", "orcid": "0000-0002-3287-121X", "clpid": "Potter-Clinton-S" } ], "abstract": "This report provides an overview of the discussions, presentations, and consensus thinking from the Workshop on Smart Data Collection for CryoEM held at the New York Structural Biology Center on April 6\u20137, 2022. The goal of the workshop was to address next generation data collection strategies that integrate machine learning and real-time processing into the workflow to reduce or eliminate the need for operator intervention.", "doi": "10.1016/j.jsb.2022.107913", "issn": "1047-8477", "publisher": "Elsevier", "publication": "Journal of Structural Biology", "publication_date": "2022-12", "series_number": "4", "volume": "214", "issue": "4", "pages": "Art. No. 107913" }, { "id": "authors:yzjs7-1cv55", "collection": "authors", "collection_id": "yzjs7-1cv55", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211105-210618923", "type": "article", "title": "Montage electron tomography of vitrified specimens", "author": [ { "family_name": "Peck", "given_name": "Ariana", "orcid": "0000-0002-5940-3897", "clpid": "Peck-Ariana" }, { "family_name": "Carter", "given_name": "Stephen D.", "orcid": "0000-0002-4237-4276", "clpid": "Carter-Stephen-D" }, { "family_name": "Mai", "given_name": "Huanghao", "orcid": "0000-0003-2278-0768", "clpid": "Mai-Huanghao" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Burt", "given_name": "Alister", "orcid": "0000-0002-9341-2295", "clpid": "Burt-Alister" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "Cryo-electron tomography provides detailed views of macromolecules in situ. However, imaging a large field of view to provide more cellular context requires reducing magnification during data collection, which in turn restricts the resolution. To circumvent this trade-off between field of view and resolution, we have developed a montage data collection scheme that uniformly distributes the dose throughout the specimen. In this approach, sets of slightly overlapping circular tiles are collected at high magnification and stitched to form a composite projection image at each tilt angle. These montage tilt-series are then reconstructed into massive tomograms with a small pixel size but a large field of view. For proof-of-principle, we applied this method to the thin edge of HeLa cells. Thon rings to better than 10 \u00c5 were detected in the montaged tilt-series, and diverse cellular features were observed in the resulting tomograms. These results indicate that the additional dose required by this technique is not prohibitive to performing structural analysis to intermediate resolution across a large field of view. We anticipate that montage tomography will prove particularly useful for lamellae, increase the likelihood of imaging rare cellular events, and facilitate visual proteomics.", "doi": "10.1016/j.jsb.2022.107860", "pmcid": "PMC10081539", "issn": "1047-8477", "publisher": "Elsevier", "publication": "Journal of Structural Biology", "publication_date": "2022-06", "series_number": "2", "volume": "214", "issue": "2", "pages": "107860" }, { "id": "authors:n3w6m-k5b80", "collection": "authors", "collection_id": "n3w6m-k5b80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200522-113331410", "type": "article", "title": "Rapid tilt-series method for cryo-electron tomography: Characterizing stage behavior during FISE acquisition", "author": [ { "family_name": "Chreifi", "given_name": "Georges", "orcid": "0000-0003-4194-1694", "clpid": "Chreifi-Georges" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "We and others recently developed rapid tilt-series acquisition methods for cryo-electron tomography on a Titan Krios G3i equipped with a single axis holder and a K-series direct electron detector and showed that one of these, the fast-incremental single exposure (FISE) method, significantly accelerates tilt-series acquisition when compared to traditional methods while preserving the quality of the images. Here, we characterize the behavior of our single axis holder in detail during a FISE experiment to optimally balance data quality with speed. We explain our methodology in detail so others can characterize their own stages, and conclude with recommendations for projects with different resolution goals.", "doi": "10.1016/j.jsb.2021.107716", "pmcid": "PMC8217199", "issn": "1047-8477", "publisher": "Elsevier", "publication": "Journal of Structural Biology", "publication_date": "2021-06", "series_number": "2", "volume": "213", "issue": "2", "pages": "Art. No. 107716" }, { "id": "authors:3r2p1-tan16", "collection": "authors", "collection_id": "3r2p1-tan16", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210125-082358436", "type": "article", "title": "Measuring gas vesicle dimensions by electron microscopy", "author": [ { "family_name": "Dutka", "given_name": "Przemys\u0142aw", "orcid": "0000-0003-3819-1618", "clpid": "Dutka-Przemys\u0142aw" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Metskas", "given_name": "Lauren Ann", "orcid": "0000-0002-8073-6960", "clpid": "Metskas-Lauren-Ann" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Hurt", "given_name": "Robert C.", "orcid": "0000-0002-4347-6901", "clpid": "Hurt-Robert-C" }, { "family_name": "Lu", "given_name": "George J.", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Gas vesicles (GVs) are cylindrical or spindle\u2010shaped protein nanostructures filled with air and used for flotation by various cyanobacteria, heterotrophic bacteria, and Archaea. Recently, GVs have gained interest in biotechnology applications due to their ability to serve as imaging agents and actuators for ultrasound, magnetic resonance and several optical techniques. The diameter of GVs is a crucial parameter contributing to their mechanical stability, buoyancy function and evolution in host cells, as well as their properties in imaging applications. Despite its importance, reported diameters for the same types of GV differ depending on the method used for its assessment. Here, we provide an explanation for these discrepancies and utilize electron microscopy (EM) techniques to accurately estimate the diameter of the most commonly studied types of GVs. We show that during air drying on the EM grid, GVs flatten, leading to a ~1.5\u2010fold increase in their apparent diameter. We demonstrate that GVs' diameter can be accurately determined by direct measurements from cryo\u2010EM samples or alternatively indirectly derived from widths of flat collapsed and negatively stained GVs. Our findings help explain the inconsistency in previously reported data and provide accurate methods to measure GVs dimensions.", "doi": "10.1002/pro.4056", "pmcid": "PMC8040859", "issn": "0961-8368", "publisher": "Wiley", "publication": "Protein Science", "publication_date": "2021-05", "series_number": "5", "volume": "30", "issue": "5", "pages": "1081-1086" }, { "id": "authors:nptj8-m3102", "collection": "authors", "collection_id": "nptj8-m3102", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190531-091859930", "type": "article", "title": "Repurposing a chemosensory macromolecular machine", "author": [ { "family_name": "Ortega", "given_name": "Davi R.", "orcid": "0000-0002-8344-2335", "clpid": "Ortega-Davi-R" }, { "family_name": "Yang", "given_name": "Wen", "clpid": "Yang-Wen" }, { "family_name": "Subramanian", "given_name": "Poorna", "clpid": "Subramanian-Poorna" }, { "family_name": "Mann", "given_name": "Petra", "clpid": "Mann-Petra" }, { "family_name": "Kjaer", "given_name": "Andreas", "orcid": "0000-0002-0096-5764", "clpid": "Kj\u00e6r-Andreas" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Watts", "given_name": "Kylie J.", "orcid": "0000-0002-8072-2745", "clpid": "Watta-Kylie-J" }, { "family_name": "Pirbadian", "given_name": "Sahand", "clpid": "Pirbadian-Sahand" }, { "family_name": "Collins", "given_name": "David A.", "clpid": "Collins-David-A" }, { "family_name": "Kooger", "given_name": "Romain", "orcid": "0000-0001-8768-1870", "clpid": "Kooger-Romain" }, { "family_name": "Kalyuzhnaya", "given_name": "Marina G.", "orcid": "0000-0002-9058-7794", "clpid": "Kalyuzhnaya-Marina-G" }, { "family_name": "Ringgaard", "given_name": "Simon", "clpid": "Ringgaard-Simon" }, { "family_name": "Briegel", "given_name": "Ariane", "orcid": "0000-0003-3733-3725", "clpid": "Briegel-Ariane" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "How complex, multi-component macromolecular machines evolved remains poorly understood. Here we reveal the evolutionary origins of the chemosensory machinery that controls flagellar motility in Escherichia coli. We first identify ancestral forms still present in Vibrio cholerae, Pseudomonas aeruginosa, Shewanella oneidensis and Methylomicrobium alcaliphilum, characterizing their structures by electron cryotomography and finding evidence that they function in a stress response pathway. Using bioinformatics, we trace the evolution of the system through \u03b3-Proteobacteria, pinpointing key evolutionary events that led to the machine now seen in E. coli. Our results suggest that two ancient chemosensory systems with different inputs and outputs (F6 and F7) existed contemporaneously, with one (F7) ultimately taking over the inputs and outputs of the other (F6), which was subsequently lost.", "doi": "10.1038/s41467-020-15736-5", "pmcid": "PMC7184735", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2020-04-27", "volume": "11", "pages": "Art. No. 2041" }, { "id": "authors:mtxf5-4e634", "collection": "authors", "collection_id": "mtxf5-4e634", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190219-101505920", "type": "article", "title": "Cryo-Electron Tomography, Faster: Development of a Fast-Incremental Tilting Scheme for Rapid Tomogram Acquisition", "author": [ { "family_name": "Chreifi", "given_name": "Georges", "clpid": "Chreifi-G" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Metskas", "given_name": "Lauren Ann", "orcid": "0000-0002-8073-6960", "clpid": "Metskas-L-A" }, { "family_name": "Mastronarde", "given_name": "David", "clpid": "Mastronarde-D-N" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "Cryo-electron microscopy enables high-resolution imaging for both protein structure determination and cellular imaging studies. When a sample's ultrastructure is unique, cryo-electron tomography can generate a volume image from a single sample, allowing the study of cellular architecture or polymorphic viruses. This technique requires tilting the microscope stage between each exposure, such that a collection of exposures is built into a stack that can be reconstructed into a three-dimensional volume. Proteins within these volumes can be averaged, with sub-tomogram averaged structures capable of reaching high resolution. However, each tomogram can require between 20-60 minutes of data collection time, restricting the number of tomograms that a user can collect in time-limited microscopy sessions. As the final resolution of sub-tomogram averages is dependent upon the number of particles in the dataset, the number of tomograms collected is severely limiting in cases where protein copy number is low.\n\nThe Jensen lab has developed a \"fast-incremental\" tilt scheme, whereby a single tomogram can be collected in 3-10 minutes. An FEI Titan Krios cryo-electron microscope and Gatan K2 camera are operated in continuous acquisition mode, using SerialEM software to blank the electron beam during stage movement; the resulting acquisition is similar in geometry and exposure to a conventional tomogram. We find that the precision of a single-tilt stage and a camera with fast frame capture rates and high sensitivity compensate for the lack of time-consuming stage tracking and adjustments during data collection, to a resolution of roughly 2.5 nm. Further hardware and software development will improve the resolution and utility of this method.", "doi": "10.1016/j.bpj.2018.11.3091", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2019-02-15", "series_number": "3", "volume": "116", "issue": "3", "pages": "575a" }, { "id": "authors:vk9w8-sn881", "collection": "authors", "collection_id": "vk9w8-sn881", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181107-100852395", "type": "article", "title": "Rapid Tilt-Series Acquisition for Electron Cryotomography", "author": [ { "family_name": "Chreifi", "given_name": "Georges", "orcid": "0000-0003-4194-1694", "clpid": "Chreifi-Georges" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Metskas", "given_name": "Lauren Ann", "orcid": "0000-0002-8073-6960", "clpid": "Metskas-Lauren-Ann" }, { "family_name": "Kaplan", "given_name": "Mohammed", "orcid": "0000-0002-0759-0459", "clpid": "Kaplan-Mohammed" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a tilt-series in seconds, but with loss of details finer than \u223c4\u202fnm. We also demonstrate a fast-incremental method that can record a tilt-series several-fold faster than current methods and with similar resolution. We characterize the utility of both methods in real biological electron cryotomography workflows. We identify opportunities for further improvements in hardware and software and speculate on the impact such advances could have on structural biology.", "doi": "10.1016/j.jsb.2018.12.008", "pmcid": "PMC6389375", "issn": "1047-8477", "publisher": "Elsevier", "publication": "Journal of Structural Biology", "publication_date": "2019-02-01", "series_number": "2", "volume": "205", "issue": "2", "pages": "163-169" }, { "id": "authors:6h5mv-2eg62", "collection": "authors", "collection_id": "6h5mv-2eg62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180227-074921090", "type": "article", "title": "Electron Cryotomography of Mycoplasma pneumoniae Mutants Correlates Terminal Organelle Architectural Features and Function", "author": [ { "family_name": "Krause", "given_name": "Duncan C.", "orcid": "0000-0003-3548-0422", "clpid": "Krause-D-C" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Shi", "given_name": "Jian", "orcid": "0000-0003-3810-5302", "clpid": "Shi-Jian-CELLBIO" }, { "family_name": "Jensen", "given_name": "Ashley", "clpid": "Jensen-A-J" }, { "family_name": "Sheppard", "given_name": "Edward S.", "clpid": "Sheppard-E-S" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "The Mycoplasma pneumoniae terminal organelle functions in adherence and gliding motility and is comprised of at least eleven substructures. We used electron cryotomography to correlate impaired gliding and adherence function with changes in architecture in diverse terminal organelle mutants. All eleven substructures were accounted for in the prkC, prpC, and P200 mutants, and variably so for the HMW3 mutant. Conversely, no terminal organelle substructures were evident in HMW1 and HMW2 mutants. The P41 mutant exhibits a terminal organelle detachment phenotype and lacked the bowl element normally present at the terminal organelle base. Complementation restored this substructure, establishing P41 as either a component of the bowl element or required for its assembly or stability, and that this bowl element is essential to anchor the terminal organelle but not for leverage in gliding. Mutants II-3, III-4, and topJ exhibited a visibly lower density of protein knobs on the terminal organelle surface. Mutants II-3 and III-4 lack accessory proteins required for a functional adhesin complex, while the topJ mutant lacks a DnaJ-like co-chaperone essential for its assembly. Taken together, these observations expand our understanding of the roles of certain terminal organelle proteins in the architecture and function of this complex structure.", "doi": "10.1111/mmi.13937", "pmcid": "PMC5912986", "issn": "0950-382X", "publisher": "Wiley", "publication": "Molecular Microbiology", "publication_date": "2018-05", "series_number": "3", "volume": "108", "issue": "3", "pages": "306-318" }, { "id": "authors:dv6qd-01798", "collection": "authors", "collection_id": "dv6qd-01798", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170616-093425610", "type": "article", "title": "Uncharacterized bacterial structures revealed by electron cryotomography", "author": [ { "family_name": "Dobro", "given_name": "Megan J.", "orcid": "0000-0002-6464-3932", "clpid": "Dobro-M-J" }, { "family_name": "Oikonomou", "given_name": "Catherine M.", "orcid": "0000-0003-2312-4746", "clpid": "Oikonomou-C-M" }, { "family_name": "Piper", "given_name": "Aidan", "clpid": "Piper-Aidan" }, { "family_name": "Cohen", "given_name": "John", "orcid": "0000-0003-1772-8236", "clpid": "Cohen-John-J" }, { "family_name": "Guo", "given_name": "Kylie", "clpid": "Guo-Kylie" }, { "family_name": "Jensen", "given_name": "Taylor", "orcid": "0000-0002-7503-9079", "clpid": "Jensen-Taylor" }, { "family_name": "Tadayon", "given_name": "Jahan", "orcid": "0000-0002-2075-6345", "clpid": "Tadayon-J" }, { "family_name": "Donermeyer", "given_name": "Joseph", "clpid": "Donermeyer-J" }, { "family_name": "Park", "given_name": "Yeram", "orcid": "0000-0002-6553-5722", "clpid": "Park-Yeram" }, { "family_name": "Solis", "given_name": "Benjamin A.", "orcid": "0000-0002-6428-2903", "clpid": "Solis-B-A" }, { "family_name": "Kj\u00e6r", "given_name": "Andreas", "orcid": "0000-0002-0096-5764", "clpid": "Kj\u00e6r-Andreas" }, { "family_name": "Jewett", "given_name": "Andrew I.", "orcid": "0000-0002-6252-9888", "clpid": "Jewett-A-I" }, { "family_name": "McDowall", "given_name": "Alasdair W.", "clpid": "McDowall-A-W" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Chang", "given_name": "Yi-Wei", "orcid": "0000-0003-2391-473X", "clpid": "Chang-Yi-Wei" }, { "family_name": "Shi", "given_name": "Jian", "orcid": "0000-0003-3810-5302", "clpid": "Shi-Jian-CELLBIO" }, { "family_name": "Subramanian", "given_name": "Poorna", "clpid": "Subramanian-Poorna" }, { "family_name": "Iancu", "given_name": "Cristina V.", "orcid": "0000-0002-7352-9226", "clpid": "Iancu-C-V" }, { "family_name": "Li", "given_name": "Zhuo", "clpid": "Li-Zhuo" }, { "family_name": "Briegel", "given_name": "Ariane", "orcid": "0000-0003-3733-3725", "clpid": "Briegel-Ariane" }, { "family_name": "Tocheva", "given_name": "Elitza I.", "orcid": "0000-0002-4869-8319", "clpid": "Tocheva-E-I" }, { "family_name": "Pilhofer", "given_name": "Martin", "clpid": "Pilhofer-M" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "Electron cryotomography (ECT) can reveal the native structure and arrangement of macromolecular complexes inside intact cells. This technique has greatly advanced our understanding of the ultrastructure of bacterial cells. We now view bacteria as structurally complex assemblies of macromolecular machines rather than as undifferentiated bags of enzymes. To date, our group has applied ECT to nearly 90 different bacterial species, collecting more than 15,000 cryotomograms. In addition to known structures, we have observed, to our knowledge, several uncharacterized features in these tomograms. Some are completely novel structures; others expand the features or species range of known structure types. Here, we present a survey of these uncharacterized bacterial structures in the hopes of accelerating their identification and study, and furthering our understanding of the structural complexity of bacterial cells.", "doi": "10.1128/JB.00100-17", "pmcid": "PMC5553035", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2017-09", "series_number": "17", "volume": "199", "issue": "17", "pages": "Art. No. e00100-17" }, { "id": "authors:6zh35-62552", "collection": "authors", "collection_id": "6zh35-62552", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171020-090832839", "type": "article", "title": "Best practices for managing large CryoEM facilities", "author": [ { "family_name": "Alewijnse", "given_name": "Bart", "clpid": "Alewijnse-B" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" } ], "abstract": "This paper provides an overview of the discussion and presentations from the Workshop on the Management of Large CryoEM Facilities held at the New York Structural Biology Center, New York, NY on February 6\u20137, 2017. A major objective of the workshop was to discuss best practices for managing cryoEM facilities. The discussions were largely focused on supporting single-particle methods for cryoEM and topics included: user access, assessing projects, workflow, sample handling, microscopy, data management and processing, and user training.", "doi": "10.1016/j.jsb.2017.07.011", "pmcid": "PMC5605453", "issn": "1047-8477", "publisher": "Elsevier", "publication": "Journal of Structural Biology", "publication_date": "2017-09", "series_number": "3", "volume": "199", "issue": "3", "pages": "225-236" }, { "id": "authors:w5yjk-23d79", "collection": "authors", "collection_id": "w5yjk-23d79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150911-094720986", "type": "article", "title": "Broadly Neutralizing Antibody 8ANC195 Recognizes Closed and Open States of HIV-1 Env", "author": [ { "family_name": "Scharf", "given_name": "Louise", "clpid": "Scharf-Louise" }, { "family_name": "Wang", "given_name": "Haoqing", "orcid": "0000-0003-0277-3018", "clpid": "Wang-Haoqing" }, { "family_name": "Gao", "given_name": "Han", "clpid": "Gao-Han" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "McDowall", "given_name": "Alasdair W.", "clpid": "McDowall-Alasdair-W" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" } ], "abstract": "The HIV-1 envelope (Env) spike contains limited epitopes for broadly neutralizing antibodies (bNAbs); thus, most neutralizing antibodies are strain specific. The 8ANC195 epitope, defined by crystal and electron microscopy (EM) structures of bNAb 8ANC195 complexed with monomeric gp120 and trimeric Env, respectively, spans the gp120 and gp41 Env subunits. To investigate 8ANC195's gp41 epitope at higher resolution, we solved a 3.58 \u00c5 crystal structure of 8ANC195 complexed with fully glycosylated Env trimer, revealing 8ANC195 insertion into a glycan shield gap to contact gp120 and gp41 glycans and protein residues. To determine whether 8ANC195 recognizes the CD4-bound open Env conformation that leads to co-receptor binding and fusion, one of several known conformations of virion-associated Env, we solved EM structures of an Env/CD4/CD4-induced antibody/8ANC195 complex. 8ANC195 binding partially closed the CD4-bound trimer, confirming structural plasticity of Env by revealing a previously unseen conformation. 8ANC195's ability to bind different Env conformations suggests advantages for potential therapeutic applications.", "doi": "10.1016/j.cell.2015.08.035", "pmcid": "PMC4587768", "issn": "0092-8674", "publisher": "Cell Press", "publication": "Cell", "publication_date": "2015-09-10", "series_number": "6", "volume": "162", "issue": "6", "pages": "1379-1390" }, { "id": "authors:jwnh3-4dz84", "collection": "authors", "collection_id": "jwnh3-4dz84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140402-152401360", "type": "article", "title": "Correlated cryogenic photoactivated localization microscopy and cryo-electron tomography", "author": [ { "family_name": "Chang", "given_name": "Yi-Wei", "orcid": "0000-0003-2391-473X", "clpid": "Chang-Yi-Wei" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Tocheva", "given_name": "Elitza I.", "orcid": "0000-0002-4869-8319", "clpid": "Tocheva-E-I" }, { "family_name": "Treuner-Lange", "given_name": "Anke", "clpid": "Treuner-Lange-Anke" }, { "family_name": "L\u00f6bach", "given_name": "Stephanie", "clpid": "L\u00f6bach-Stephanie" }, { "family_name": "S\u00f8gaard-Andersen", "given_name": "Lotte", "clpid": "S\u00f8gaard-Andersen-Lotte" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "Cryo-electron tomography (CET) produces three-dimensional images of cells in a near-native state at macromolecular resolution, but identifying structures of interest can be challenging. Here we describe a correlated cryo-PALM (photoactivated localization microscopy)-CET method for localizing objects within cryo-tomograms to beyond the diffraction limit of the light microscope. Using cryo-PALM-CET, we identified multiple and new conformations of the dynamic type VI secretion system in the crowded interior of Myxococcus xanthus.", "doi": "10.1038/nmeth.2961", "pmcid": "PMC4081473", "issn": "1548-7091", "publisher": "Nature Publishing Group", "publication": "Nature Methods", "publication_date": "2014-07", "series_number": "7", "volume": "11", "issue": "7", "pages": "737-739" }, { "id": "authors:7whe5-v2e53", "collection": "authors", "collection_id": "7whe5-v2e53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110908-081125458", "type": "article", "title": "Structural diversity of bacterial flagellar motors", "author": [ { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Beeby", "given_name": "Morgan", "orcid": "0000-0001-6413-9835", "clpid": "Beeby-M-D" }, { "family_name": "Murphy", "given_name": "Gavin E.", "clpid": "Murphy-G-E" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Hendrixson", "given_name": "David R.", "clpid": "Hendrixson-D-R" }, { "family_name": "Briegel", "given_name": "Ariane", "orcid": "0000-0003-3733-3725", "clpid": "Briegel-Ariane" }, { "family_name": "Li", "given_name": "Zhuo", "clpid": "Li-Zhuo" }, { "family_name": "Shi", "given_name": "Jian", "orcid": "0000-0003-3810-5302", "clpid": "Shi-Jian-CELLBIO" }, { "family_name": "Tocheva", "given_name": "Elitza I.", "orcid": "0000-0002-4869-8319", "clpid": "Tocheva-E-I" }, { "family_name": "M\u00fcller", "given_name": "Axel", "clpid": "M\u00fcller-A" }, { "family_name": "Dobro", "given_name": "Megan J.", "orcid": "0000-0002-6464-3932", "clpid": "Dobro-M-J" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "The bacterial flagellum is one of nature's most amazing\nand well-studied nanomachines. Its cell-wall-anchored\nmotor uses chemical energy to rotate a microns-long\nfilament and propel the bacterium towards nutrients and\naway from toxins. While much is known about flagellar\nmotors from certain model organisms, their diversity\nacross the bacterial kingdom is less well characterized,\nallowing the occasional misrepresentation of the motor as\nan invariant, ideal machine. Here, we present an electron\ncryotomographical survey of flagellar motor architectures\nthroughout the Bacteria. While a conserved structural\ncore was observed in all 11 bacteria imaged, surprisingly\nnovel and divergent structures as well as different symmetries were observed surrounding the core. Correlating the motor structures with the presence and absence of particular motor genes in each organism suggested the locations of five proteins involved in the export apparatus\nincluding FliI, whose position below the C-ring was confirmed by imaging a deletion strain. The combination of\nconserved and specially-adapted structures seen here\nsheds light on how this complex protein nanomachine\nhas evolved to meet the needs of different species.", "doi": "10.1038/emboj.2011.186", "pmcid": "PMC3641884", "issn": "0261-4189", "publisher": "European Molecular Biology Organization", "publication": "EMBO Journal", "publication_date": "2011-07-20", "series_number": "14", "volume": "30", "issue": "14", "pages": "2972-2981" }, { "id": "authors:017rg-ty753", "collection": "authors", "collection_id": "017rg-ty753", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110524-100904457", "type": "article", "title": "Long helical filaments are not seen encircling cells in electron cryotomograms of rod-shaped bacteria", "author": [ { "family_name": "Swulius", "given_name": "Matthew T.", "clpid": "Swulius-M-T" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Ding", "given_name": "H. Jane", "clpid": "Ding-H-Jane" }, { "family_name": "Li", "given_name": "Zhuo", "clpid": "Li-Zhuo" }, { "family_name": "Briegel", "given_name": "Ariane", "orcid": "0000-0003-3733-3725", "clpid": "Briegel-Ariane" }, { "family_name": "Pilhofer", "given_name": "Martin", "clpid": "Pilhofer-M" }, { "family_name": "Tocheva", "given_name": "Elitza I.", "orcid": "0000-0002-4869-8319", "clpid": "Tocheva-E-I" }, { "family_name": "Lybarger", "given_name": "Suzanne R.", "clpid": "Lybarger-S-R" }, { "family_name": "Johnson", "given_name": "Tanya L.", "clpid": "Johnson-T-L" }, { "family_name": "Sandkvist", "given_name": "Maria", "clpid": "Sandkvist-M" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "How rod-shaped bacteria form and maintain their shape is an important question in bacterial cell biology. Results from fluorescent light microscopy have led many to believe that the actin homolog MreB and a number of other proteins form long helical filaments along the inner membrane of the cell. Here we show using electron cryotomography of six different rod-shaped bacterial species, at macromolecular resolution, that no long (>80 nm) helical filaments exist near or along either surface of the inner membrane. We also use correlated cryo-fluorescent light microscopy (cryo-fLM) and electron cryo-tomography (ECT) to identify cytoplasmic bundles of MreB, showing that MreB filaments are detectable by ECT. In light of these results, the structure and function of MreB must be reconsidered: instead of acting as a large, rigid scaffold that localizes cell-wall synthetic machinery, moving MreB complexes may apply tension to growing peptidoglycan strands to ensure their orderly, linear insertion.", "doi": "10.1016/j.bbrc.2011.03.062", "pmcid": "PMC3093302", "issn": "0006-291X", "publisher": "Elsevier", "publication": "Biochemical and Biophysical Research Communications", "publication_date": "2011-04-22", "series_number": "4", "volume": "407", "issue": "4", "pages": "650-655" }, { "id": "authors:vp8dj-53p82", "collection": "authors", "collection_id": "vp8dj-53p82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110804-140527126", "type": "article", "title": "Electron Cryotomography of Bacterial Cells", "author": [ { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "McDowall", "given_name": "Alasdair", "clpid": "McDowall-A-W" }, { "family_name": "Dobro", "given_name": "Megan J.", "orcid": "0000-0002-6464-3932", "clpid": "Dobro-M-J" }, { "family_name": "Briegel", "given_name": "Ariane", "orcid": "0000-0003-3733-3725", "clpid": "Briegel-Ariane" }, { "family_name": "Ladinsky", "given_name": "Mark", "orcid": "0000-0002-1036-3513", "clpid": "Ladinsky-M-S" }, { "family_name": "Shi", "given_name": "Jian", "orcid": "0000-0003-3810-5302", "clpid": "Shi-Jian-CELLBIO" }, { "family_name": "Tocheva", "given_name": "Elitza I.", "orcid": "0000-0002-4869-8319", "clpid": "Tocheva-E-I" }, { "family_name": "Beeby", "given_name": "Morgan", "orcid": "0000-0001-6413-9835", "clpid": "Beeby-M-D" }, { "family_name": "Pilhofer", "given_name": "Martin", "clpid": "Pilhofer-M" }, { "family_name": "Ding", "given_name": "H. Jane", "clpid": "Ding-H-Jane" }, { "family_name": "Li", "given_name": "Zhuo", "clpid": "Li-Zhuo" }, { "family_name": "Gan", "given_name": "Lu", "orcid": "0000-0002-8685-4896", "clpid": "Gan-Lu" }, { "family_name": "Morris", "given_name": "Dylan M.", "clpid": "Morris-D-M" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "While much is already known about the basic metabolism of bacterial cells, many fundamental questions are still surprisingly unanswered, including\nfor instance how they generate and maintain specific cell shapes, establish polarity, segregate their genomes, and divide. In order to understand\nthese phenomena, imaging technologies are needed that bridge the resolution gap between fluorescence light microscopy and higher-resolution\nmethods such as X-ray crystallography and NMR spectroscopy.\nElectron cryotomography (ECT) is an emerging technology that does just this, allowing the ultrastructure of cells to be visualized in a near-native\nstate, in three dimensions (3D), with \"macromolecular\" resolution (~4nm). In ECT, cells are imaged in a vitreous, \"frozen-hydrated\" state in a cryo\ntransmission electron microscope (cryoTEM) at low temperature (< -180\u00b0C). For slender cells (up to ~500 nm in thickness), intact cells are\nplunge-frozen within media across EM grids in cryogens such as ethane or ethane/propane mixtures. Thicker cells and biofilms can also be imaged\nin a vitreous state by first \"high-pressure freezing\" and then, \"cryo-sectioning\" them. A series of two-dimensional projection images are then\ncollected through the sample as it is incrementally tilted along one or two axes. A three-dimensional reconstruction, or \"tomogram\" can then be\ncalculated from the images. While ECT requires expensive instrumentation, in recent years, it has been used in a few labs to reveal the structures\nof various external appendages, the structures of different cell envelopes, the positions and structures of cytoskeletal filaments, and the locations\nand architectures of large macromolecular assemblies such as flagellar motors, internal compartments and chemoreceptor arrays.\nIn this video article we illustrate how to image cells with ECT, including the processes of sample preparation, data collection, tomogram\nreconstruction, and interpretation of the results through segmentation and in some cases correlation with light microscopy.", "doi": "10.3791/1943", "pmcid": "PMC3149996", "issn": "1940-087X", "publisher": "JoVE", "publication": "Journal of Visualized Experiments", "publication_date": "2010-05-06", "series_number": "39", "issue": "39", "pages": "Art. No. 1943" }, { "id": "authors:pzcsm-e6657", "collection": "authors", "collection_id": "pzcsm-e6657", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091019-151620276", "type": "article", "title": "Universal architecture of bacterial chemoreceptor arrays", "author": [ { "family_name": "Briegel", "given_name": "Ariane", "orcid": "0000-0003-3733-3725", "clpid": "Briegel-Ariane" }, { "family_name": "Ortega", "given_name": "Davi R.", "orcid": "0000-0002-8344-2335", "clpid": "Ortega-D-R" }, { "family_name": "Tocheva", "given_name": "Elitza I.", "orcid": "0000-0002-4869-8319", "clpid": "Tocheva-E-I" }, { "family_name": "Wuichet", "given_name": "Kristin", "clpid": "Wuichet-K" }, { "family_name": "Li", "given_name": "Zhuo", "clpid": "Li-Zhuo" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "M\u00fcller", "given_name": "Axel", "clpid": "M\u00fcller-A" }, { "family_name": "Iancu", "given_name": "Cristina V.", "orcid": "0000-0002-7352-9226", "clpid": "Iancu-C-V" }, { "family_name": "Murphy", "given_name": "Gavin E.", "clpid": "Murphy-G-E" }, { "family_name": "Dobro", "given_name": "Megan J.", "orcid": "0000-0002-6464-3932", "clpid": "Dobro-M-J" }, { "family_name": "Zhulin", "given_name": "Igor B.", "orcid": "0000-0002-6708-5323", "clpid": "Zhulin-I-B" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "Chemoreceptors are key components of the high-performance signal transduction system that controls bacterial chemotaxis. Chemoreceptors are typically localized in a cluster at the cell pole, where interactions among the receptors in the cluster are thought to contribute to the high sensitivity, wide dynamic range, and precise adaptation of the signaling system. Previous structural and genomic studies have produced conflicting models, however, for the arrangement of the chemoreceptors in the clusters. Using whole-cell electron cryo-tomography, here we show that chemoreceptors of different classes and in many different species representing several major bacterial phyla are all arranged into a highly conserved, 12-nm hexagonal array consistent with the proposed \"trimer of dimers\" organization. The various observed lengths of the receptors confirm current models for the methylation, flexible bundle, signaling, and linker sub-domains in vivo. Our results suggest that the basic mechanism and function of receptor clustering is universal among bacterial species and was thus conserved during evolution.", "doi": "10.1073/pnas.0905181106", "pmcid": "PMC2761316", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2009-10-06", "series_number": "40", "volume": "106", "issue": "40", "pages": "17181-17186" }, { "id": "authors:6t07x-mqc80", "collection": "authors", "collection_id": "6t07x-mqc80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GANpnas08", "type": "article", "title": "Molecular organization of Gram-negative peptidoglycan", "author": [ { "family_name": "Gan", "given_name": "Lu", "orcid": "0000-0002-8685-4896", "clpid": "Gan-Lu" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "The stress-bearing component of the bacterial cell wall -\u2014 a multi-gigadalton bag-like molecule called the sacculus -\u2014 is synthesized from peptidoglycan. Whereas the chemical composition and the 3-dimensional structure of the peptidoglycan subunit (in at least one conformation) are known, the architecture of the assembled sacculus is not. Four decades' worth of biochemical and electron microscopy experiments have resulted in two leading 3-D peptidoglycan models: \"Layered\" and \"Scaffold\", in which the glycan strands are parallel and perpendicular to the cell surface, respectively. Here we resolved the basic architecture of purified, frozen-hydrated sacculi through electron cryotomography. In the Gram-negative sacculus, a single layer of glycans lie parallel to the cell surface, roughly perpendicular to the long axis of the cell, encircling the cell in a disorganized hoop-like fashion.", "doi": "10.1073/pnas.0808035105", "pmcid": "PMC2596242", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2008-12-02", "series_number": "48", "volume": "105", "issue": "48", "pages": "18953-18957" }, { "id": "authors:x46d6-drx71", "collection": "authors", "collection_id": "x46d6-drx71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160816-122128144", "type": "article", "title": "Ultrafast Electron Crystallography. 2. Surface Adsorbates of Crystalline Fatty Acids and Phospholipids", "author": [ { "family_name": "Seidel", "given_name": "Marco T.", "clpid": "Seidel-M-T" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "abstract": "In this account, the second in this series, we report our detailed studies of the structures and dynamics of adsorbates of crystalline fatty acids and phospholipids, using ultrafast electron crystallography (UEC). These macromolecules serve as model systems for biomembranes and allow for systematic studies under controlled conditions. The systems investigated are arachidic (eicosanoic) acid and dimyristoyl phosphatidic acid (DMPA), deposited on a substrate by the Langmuir\u2212Blodgett technique. We studied these systems in monolayer, bilayer, and multilayer structures, and under different conditions (pH, pressure, and temperature) and on different substrates (hydrophobic and hydrophilic). The subunit cell \u2212CH_2\u2212CH_2\u2212CH_2\u2212 distances were determined for all structures. For fatty acid samples, the structure is orthorhombic, and a_0 and b_0 have the values, depending on conditions, of 4.7\u22124.9 \u00c5 and 8.0\u22128.9 \u00c5, respectively. The c_0 value is 2.54 \u00c5 and for a given sample the accuracy is milliangstrom. Structural dynamics, after an ultrafast temperature jump in the underlying substrate, were studied by observing changes of the diffraction patterns:\u2009 Bragg spot position, intensity, width, and the rocking curves. All structures exhibit a coherent anisotropic nonequilibrium expansion along the aliphatic chains, accompanied by transient structural ordering on the ultrafast time-scale. This wave-type, not diffusive, motion is followed by contraction and restructuring at longer times due to energy redistribution and diffusion. The transient behavior is entirely different from that reported here at equilibrium temperatures, in the range of 100\u2212380 K. From these results, we are able to draw a general picture for the structural dynamics of amphiphilic chain molecules and elucidate the important role of nonequilibrium behavior at short times.", "doi": "10.1021/jp0674672", "issn": "1932-7447", "publisher": "American Chemical Society", "publication": "Journal of Physical Chemistry C", "publication_date": "2007-04-05", "series_number": "13", "volume": "111", "issue": "13", "pages": "4920-4938" }, { "id": "authors:fxfp9-xme69", "collection": "authors", "collection_id": "fxfp9-xme69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160816-122128915", "type": "article", "title": "Ultrafast Electron Crystallography of Phospholipids", "author": [ { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Seidel", "given_name": "Marco T.", "clpid": "Seidel-M-T" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "abstract": "The structure and dynamics of monolayer and bilayer (see picture) phospholipids have been studied with spatiotemporal resolutions by ultrafast electron crystallography. The expansion and restructuring of the chains were observed after a femtosecond temperature jump in the substrate, and a transient structural ordering was revealed. The atomic forces were identified to be coherent in the non-equilibrium state of the assembly.", "doi": "10.1002/anie.200601778", "issn": "1433-7851", "publisher": "Wiley", "publication": "Angewandte Chemie International Edition", "publication_date": "2006-08-04", "series_number": "31", "volume": "45", "issue": "31", "pages": "5154-5158" }, { "id": "authors:8v7kw-q4w42", "collection": "authors", "collection_id": "8v7kw-q4w42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CHEpnas05b", "type": "article", "title": "Atomic-scale dynamical structures of fatty acid bilayers observed by ultrafast electron crystallography", "author": [ { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Seidel", "given_name": "Marco T.", "clpid": "Seidel-M-T" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "abstract": "The structure and dynamics of a biological model bilayer are reported with atomic-scale resolution by using ultrafast electron crystallography. The bilayer was deposited as a Langmuir-Blodgett structure of arachidic (eicosanoic) fatty acids with the two chains containing 40 carbon atoms (50 \u00c5), on a hydrophobic substrate, the hydrogen terminated silicon(111) surface. We determined the structure of the 2D assembly, establishing the orientation of the chains and the subunit cell of the CH2 distances: a0 = 4.7 \u00c5, b0 = 8.0 \u00c5, and c0 = 2.54 \u00c5. For structural dynamics, the diffraction frames were taken every 1 picosecond after a femtosecond temperature jump. The observed motions, with sub-\u00c5 resolution and monolayer sensitivity, clearly indicate the coherent anisotropic expansion of the bilayer solely along the aliphatic chains, followed by nonequilibrium contraction and restructuring at longer times. This motion is indicative of a nonlinear behavior among the anharmonically coupled bonds on the ultrashort time scale and energy redistribution and diffusion on the longer time scale. The ability to observe such atomic motions of complex structures and at interfaces is a significant leap forward for the determination of macromolecular dynamical structures by using ultrafast electron crystallography.", "doi": "10.1073/pnas.0504022102", "pmcid": "PMC1150297", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2005-06-21", "series_number": "25", "volume": "102", "issue": "25", "pages": "8854-8859" }, { "id": "authors:30kxr-q3854", "collection": "authors", "collection_id": "30kxr-q3854", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160817-092916920", "type": "article", "title": "Ultrafast Electron Crystallography of Surface Structural Dynamics with Atomic-Scale Resolution", "author": [ { "family_name": "Vigliotti", "given_name": "Franco", "clpid": "Vigliotti-F" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Ruan", "given_name": "Chong-Yu", "clpid": "Ruan-Chong-Yu" }, { "family_name": "Lobastov", "given_name": "Vladimir A.", "clpid": "Lobastov-V-A" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "abstract": "A formidable contender to X-ray diffraction is ultrafast electron crystallography. Whereas the former is more suited to investigate the bulk of the substrate, the time, length, and sensitivity scales of electron crystallography provide powerful and complementary information on atomic-scale structural dynamics at the surface (see diffraction image of GaAs crystal).", "doi": "10.1002/anie.200453983", "issn": "1433-7851", "publisher": "Wiley", "publication": "Angewandte Chemie International Edition", "publication_date": "2004-05-10", "series_number": "20", "volume": "43", "issue": "20", "pages": "2705-2709" }, { "id": "authors:gdpe5-yh369", "collection": "authors", "collection_id": "gdpe5-yh369", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141120-153340550", "type": "article", "title": "Ultrafast Electron Crystallography of Interfacial Water", "author": [ { "family_name": "Ruan", "given_name": "Chong-Yu", "clpid": "Ruan-Chong-Yu" }, { "family_name": "Lobastov", "given_name": "Vladimir A.", "clpid": "Lobastov-V-A" }, { "family_name": "Vigliotti", "given_name": "Franco", "clpid": "Vigliotti-F" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "abstract": "We report direct determination of the structures and dynamics of interfacial water on a hydrophilic surface with atomic-scale resolution using ultrafast electron crystallography. On the nanometer scale, we observed the coexistence of ordered surface water and crystallite-like ice structures, evident in the superposition of Bragg spots and Debye-Scherrer rings. The structures were determined to be dominantly cubic, but each undergoes different dynamics after the ultrafast substrate temperature jump. From changes in local bond distances (OH\u00b7\u00b7O and O\u00b7\u00b7\u00b7O) with time, we elucidated the structural changes in the far-from-equilibrium regime at short times and near-equilibration at long times.", "doi": "10.1126/science.1094818", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2004-04-02", "series_number": "5667", "volume": "304", "issue": "5667", "pages": "80-84" }, { "id": "authors:bskty-eta84", "collection": "authors", "collection_id": "bskty-eta84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:RUApnas04", "type": "article", "title": "Ultrafast electron crystallography: Transient structures of molecules, surfaces, and phase transitions", "author": [ { "family_name": "Ruan", "given_name": "Chong-Yu", "clpid": "Ruan-Chong-Yu" }, { "family_name": "Vigliotti", "given_name": "Franco", "clpid": "Vigliotti-F" }, { "family_name": "Lobastov", "given_name": "Vladimir A.", "clpid": "Lobastov-V-A" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "abstract": "The static structure of macromolecular assemblies can be mapped out with atomic-scale resolution by using electron diffraction and microscopy of crystals. For transient nonequilibrium structures, which are critical to the understanding of dynamics and mechanisms, both spatial and temporal resolutions are required; the shortest scales of length (0.1\u20131 nm) and time (10^\u201313 to 10^\u201312 s) represent the quantum limit, the nonstatistical regime of rates. Here, we report the development of ultrafast electron crystallography for direct determination of structures with submonolayer sensitivity. In these experiments, we use crystalline silicon as a template for different adsorbates: hydrogen, chlorine, and trifluoroiodomethane. We observe the coherent restructuring of the surface layers with subangstrom displacement of atoms after the ultrafast heat impulse. This nonequilibrium dynamics, which is monitored in steps of 2 ps (total change <=10 ps), contrasts that of the nanometer substrate. The effect of adsorbates and the phase transition at higher fluences were also studied through the evolution of streaks of interferences, Bragg spots (and their rocking curves), and rings in the diffraction patterns. We compare these results with kinematical theory and those of x-ray diffraction developed to study bulk behaviors. The sensitivity achieved here, with the 6 orders of magnitude larger cross section than x-ray diffraction, and with the capabilities of combined spatial ({approx}0.01 \u00c5) and temporal (300\u2013600 fs) resolutions, promise diverse applications for this ultrafast electron crystallography tabletop methodology.", "doi": "10.1073/pnas.0307302101", "pmcid": "PMC337017", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2004-02-03", "series_number": "5", "volume": "101", "issue": "5", "pages": "1123-1128" } ]