Криоэлектронная микроскопия как инструмент системной биологии, структурного анализа и экспериментального воздействия на клетки. Комплексный аналитический обзор новейших работ

Автор(и)

  • Oleg V. Gradov Інститут енергетичних проблем хімічної фізики РАН, м. Москва
  • Margarita A. Gradova Інститут хімічної фізики ім. Ðœ.Ðœ. Семенова, м. Москва

DOI:

https://doi.org/10.15407/cryo24.03.193

Ключові слова:

кріоелектронна мікроскопія, кріоелектронна томографія, системна біологія, локаломіка, динаміка, структурний аналіз, in silico, мікромашинінг

Анотація

Метою даної роботи Ñ” демонÑÑ‚Ñ€Ð°Ñ†Ñ–Ñ Ð½Ð¾Ð²Ð¾Ð³Ð¾ поглÑду на кріоелектронну мікроÑкопію біологічних Ñтруктур Ñк на
проÑтий багатофакторний інÑтрумент ÑиÑтемної біології, Ñкий допуÑкає заÑтоÑÑƒÐ²Ð°Ð½Ð½Ñ Ð¹Ð¾Ð³Ð¾ Ð´Ð»Ñ ÑƒÐ»ÑŒÑ‚Ñ€Ð°Ñтруктурного позиційно-чутливого, а також динамічного аналізу в молекулÑрній цитоморфології та Ñуміжних диÑциплінах. РозглÑдаютьÑÑ Ñ€Ñ–Ð·Ð½Ñ– методи кріоелектронної аналітики та відповідні ÑиÑтемно-біологічні інтерпретації, ÑиÑÑ‚ÐµÐ¼Ð°Ñ‚Ð¸Ð·Ð°Ñ†Ñ–Ñ Ñких може бути кориÑною Ð´Ð»Ñ Ð¿Ð¾Ñ‡Ð°Ñ‚ÐºÐ¾Ð²Ð¾Ñ— поÑтановки прогреÑивних задач під Ñ‡Ð°Ñ Ð´Ð¾Ñліджень цими методами та наÑтупної обробки отриманих результатів. Показано, що ÑиÑтемніÑÑ‚ÑŒ методології кріоелектронної мікроÑкопії прÑмо кореÑпондує зі ÑиÑтемніÑÑ‚ÑŽ та багатопараметричним
характером Ñ—Ñ— аналітів у рамках ÑиÑтемної біології. Ðаведено дані щодо викориÑÑ‚Ð°Ð½Ð½Ñ ÐºÑ€Ñ–Ð¾ÐµÐ»ÐµÐºÑ‚Ñ€Ð¾Ð½Ð½Ð¾Ñ— мікроÑкопії у мікро-
Ñтруктурній обробці та мікроманіпулÑціÑÑ… на клітинах (Ñ‚. зв. micromachining), а також у розробці молекулÑрних машин. У
цьому аналітичному обзорі наведено відомоÑÑ‚Ñ– на оÑнові даних кріоелектронної мікроÑкопії оÑтанніх років.

Посилання

Abreu F., Sousa A.A., Aronova M.A. et al. Cryo-electron tomography of the magnetotactic vibrio Magnetovibrio blakemorei: insights into the biomineralization of prismatic magnetosomes. Journ Struct Biol 2013; 181(2): 162–168. CrossRef PubMed

Agirre J., Goret G., LeGoff M. et al. Cryo-electron microscopy reconstructions of triatoma virus particles: a clue to unravel genome delivery and capsid disassembly. Journ Gen Virol 2013; 94: 1058–1068. CrossRef PubMed

Ahmed A., Whitford P.C., Sanbonmatsu K.Y., Tama F. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. Journ Struct Biol 2012; 177(2): 561–570. CrossRef PubMed

Allen G.S., Stokes D.L. Modeling, docking, and fitting of atomic structures to 3D maps from cryo-electron microscopy. Meth Mol Biol 2013; 955: 229–241. CrossRef PubMed

Azuaje F. Bioinformatics and Biomarker Discovery: "Omic" Data Analysis for Personalized Medicine. Hoboken, New Jersey; 2010.

Bai X.C., Martin T.G., Scheres S.H., Dietz H. Cryo-EM structure of a 3D DNA-origami object. Proc Nat Acad Sci USA 2012; 109(49): 20012–20017. CrossRef PubMed

Bajaj C., Goswami S., Zhang Q. Detection of secondary and supersecondary structures of proteins from cryo-electron microscopy. Journ Struc Biol 2012; 177(2): 367–381. CrossRef PubMed

Balfour B.M., Goscicka T., MacKenzie J.L. et al. Combined time-lapse cinematography and immuno-electron microscopy. Anat Rec 1990; 226(4): 509–514. CrossRef PubMed

Bartesaghi A., Lecumberry F., Sapiro G., Subramaniam S. Protein secondary structure determination by constrained single-particle cryo-electron tomography. Structure 2012; 20(12): 2003–2013. CrossRef PubMed

Barton B., Rhinow D., Walter A. et al. In-focus electron microscopy of frozen-hydrated biological samples with a Boersch phase plate. Ultramicroscopy 2011; 111(12): 1696–1705. CrossRef PubMed

Bergstrцm L.M., Skoglund S., Edwards K. et al. Self-assembly in mixtures of an anionic and a cationic surfactant: a comparison between small-angle neutron scattering and cryo-transmission electron microscopy. Langmuir 2013; 29(38): 11834–11848. CrossRef PubMed

Bharat T.A., Davey N.E., Ulbrich P. et al. Structure of the immature retroviral capsid at 8A resolution by cryo-electron microscopy. Nature 2012; 487(7407): 385–389. CrossRef PubMed

Bouchet-Marquis C., Pagratis M., Kirmse R., Hoenger A. Metallothionein as a clonable high-density marker for cryo-electron microscopy. Journ Struc Biol 2012; 177(1): 119–127. CrossRef PubMed

Briegel A., Chen S., Koster A.J. et al. Correlated light and electron cryo-microscopy. Meth Enzymol 2010; 481: 317–341. CrossRef

Briggs J.A. Structural biology in situ – the potential of subtomogram averaging. Curr Opin Struct Biol 2013; 23(2): 261–267. CrossRef PubMed

Brusic V. From immunoinformatics to immunomics. Journ Bioinform Comput Biol 2003; 1: 179–181. CrossRef

Bui K.H., Ishikawa T. 3D structural analysis of flagella/cilia by cryo-electron tomography. Meth Enzymol 2013; 524: 305–323. CrossRef PubMed

Campbell M.G., Cheng A., Brilot A.F. et al. Movies of ice-embedded particles enhance resolution in electron cryomicroscopy. Structure 2012; 20(11): 1823–1828. CrossRef PubMed

Cao C., Dong X., Wu X. et al. Conserved fiber-penton base interaction revealed by nearly atomic resolution cryo-electron microscopy of the structure of adenovirus provides insight into receptor interaction. Journ Virol 2012; 86(22): 12322–12329. CrossRef PubMed

Cardone G., Heymann J.B., Steven A.C. One number does not fit all: Mapping local variations in resolution in cryo-EM reconstructions. Journ Struc Biol 2013; 184(2): 226–236. CrossRef PubMed

Carlson D.B., Gelb J., Palshin V., Evans J.E. Laboratory-based cryogenic soft X-ray tomography with correlative cryo-light and electron microscopy. Micros Microanal 2013; 19(1): 22–29. CrossRef PubMed

Caston J.R. Conventional electron microscopy, cryo-electron microscopy and cryo-electron tomography of viruses. Subcell Biochem 2013; 68: 79–115. CrossRef PubMed

Chan K.Y., Trabuco L.G., Schreiner E., Schulten K. Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method. Biopolymers 2012; 97(9): 678–686. CrossRef PubMed

Comolli L.R., Duarte R., Baum D. et al. A portable cryo-plunger for on-site intact cryogenic microscopy sample preparation in natural environments. Micros Res Tech 2012; 75(6): 829–836. CrossRef PubMed

Cong Y., Schröder G.F., Meyer A.S. et al. Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle. EMBO Journ 2012; 31(3): 720–730. CrossRef PubMed

Crauste-Manciet S., Larquet E., Khawand K. et al. Lipidic spherulites: Formulation optimisation by paired optical and cryo-electron microscopy. Eur Journ Pharm Biopharm 2013; 85(3): 1088–1094. CrossRef PubMed

De Vries S.J., Zacharias M. ATTRACT-EM: a new method for the computational assembly of large molecular machines using cryo-EM maps. PLoS One 2012; 7(12): e49733.

De Winter D.A., Mesman R.J., Hayles M.F. et al. In-situ integrity control of frozen-hydrated, vitreous lamellas prepared by the cryo-focused ion beam scanning electron microscope. Journ Struc Biol 2013; 183(1): 11–18. CrossRef PubMed

Diebolder C.A., Koster A.J., Koning R.I. Pushing the resolution limits in cryoelectron tomography of biological structures. Journ Microsc 2012; 248(1): 1–5. CrossRef PubMed

DiMaio F., Zhang J., Chiu W., Baker D. Cryo-EM model validation using independent map reconstructions. Prot Sci 2013; 22(6): 865–868. CrossRef PubMed

Dubochet J. Cryo-EM – the first thirty years. Journ Microsc 2012; 245(3): 221–224. CrossRef

Duke E.M., Razi M., Weston A. et al. Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM). Ultramicroscopy 2014; 143: 77–87. CrossRef PubMed

Eibauer M., Hoffmann C., Plitzko J.M. et al. Unraveling the structure of membrane proteins in situ by transfer function corrected cryo-electron tomography. Journ Struct Biol 2012; 180(3): 488–496. CrossRef PubMed

Elber R. Watching biomolecular machines in action. Structure 2010; 18(4): 415–416. CrossRef PubMed

Elmlund H., Elmlund D., Bengio S. PRIME: probabilistic initial 3D model generation for single-particle cryo-electron microscopy. Structure 2013; 21(8): 1299–1306. CrossRef PubMed

Falkner B., Schroder G.F. Cross-validation in cryo-EM-based structural modeling. Proc Nat Acad Sci USA 2013; 110(22): 8930–8935. CrossRef PubMed

Fitzpatrick A.W., Lorenz U.J., Vanacore G.M., Zewail A.H. 4D cryo-electron microscopy of proteins. Journ Am Chem Soc 2013; 135(51): 19123–19126. CrossRef PubMed

Forrester J.S., Milne S.B., Ivanova P.T., Brown H.A. Computational lipidomics: a multi-plexed analysis of dynamic changes in membrane lipid composition during signal transduc-tion. Mol Pharmacol 2004; 65(4): 813–821. CrossRef PubMed

Frank J. Story in a sample – the potential (and limitations) of cryo-electron microscopy applied to molecular machines. Biopolymers 2013; 99(11): 832–836. CrossRef PubMed

Fujiyoshi Y. Low dose techniques and cryo-electron microscopy. Meth Mol Biol 2013; 955: 103–118. CrossRef PubMed

Fukuda Y., Nagayama K. Zernike phase contrast cryo-electron tomography of whole mounted frozen cells. Journ Struc Biol 2012; 177(2): 484–489. CrossRef PubMed

Garewal M., Zhang L., Ren G. Optimized negative-staining protocol for examining lipid-protein interactions by electron microscopy. Meth Mol Biol 2013; 974: 111–118. CrossRef PubMed

Gopalakrishnan G., Yam P.T., Madwar C. et al. Label-free visualization of ultrastructural features of artificial synapses via cryo-EM. ACS Chem Neurosci 2011; 2(12): 700–704. CrossRef PubMed

Grélard A., Guichard P., Bonnafous P. et al. Hepatitis B subvirus particles display both a fluid bilayer membrane and a strong resistance to freeze drying: a study by solid-state NMR, light scattering, and cryo-electron microscopy/tomography. FASEB Journ 2013; 27(10): 4316–4326. CrossRef PubMed

Greunz T., Strauß B., Schausberger S.E. et al. Cryo ultra-low-angle microtomy for XPS-depth profiling of organic coatings. Anal Bioanal Chem 2013; 405(22): 7153–7160. CrossRef PubMed

Grigorieff N. Direct detection pays off for electron cryo-microscopy. ELIFE 2013; 2: e00573.

Guesdon A., Blestel S., Kervrann C., Chrétien D. Single versus dual-axis cryo-electron tomography of microtubules assembled in vitro: limits and perspectives. Journ Struc Biol 2013; 181(2): 169–178. CrossRef PubMed

Gyobu N. Grid preparation for cryo-electron microscopy. Meth Mol Biol 2013; 955: 119–128. CrossRef PubMed

Han H.M., Bouchet-Marquis C., Huebinger J., Grabenbauer M. Golgi apparatus analyzed by cryo-electron microscopy. Histochem Cell Biol 2013; 140(4): 369–381. CrossRef PubMed

Han H.M., Huebinger J., Grabenbauer M. Self-pressurized rapid freezing (SPRF) as a simple fixation method for cryo-electron microscopy of vitreous sections. Journ Struc Biol 2012; 178(2): 84–87. CrossRef PubMed

Heymann J.B., Winkler D.C., Yim Y.I. et al. Clathrin-coated vesicles from brain have small payloads: a cryo-electron tomographic study. Journ Struc Biol 2013; 184(1): 43–51. CrossRef PubMed

Hoang T.V., Cavin X., Schultz P., Ritchie D.W. gEMpicker: A highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy. BMC Struct Biol 2013; 13(25): 1–10. CrossRef

Hoofnagle A.N., Heinecke J.W. Lipoproteomics: using mass spectrometry-based proteomics to explore the assembly, structure, and function of lipoproteins. Journ Lipid Res 2009; 50(10): 1967–1975. CrossRef PubMed

Hrabe T., Chen Y., Pfeffer S. et al. PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis. Journ Struct Biol 2012; 178(2): 177–188. CrossRef PubMed

Hsieh C., Schmelzer T., Kishchenko G. et al. Practical workflow for cryo focused-ion-beam milling of tissues and cells for cryo-TEM tomography. Journ Struc Biol 2014; 185(1): 32–41. CrossRef PubMed

Huisken J., Stainier D.Y. Selective plane illumination microscopy techniques in developmental biology. Development 2009; 136(12): 1963–1975. CrossRef PubMed

Iijima H., Fukuda Y., Arai Y. et al. Hybrid fluorescence and electron cryo-microscopy for simultaneous electron and photon imaging. Journ Struc Biol 2014; 185(1): 107–115. CrossRef PubMed

Johnson M.C., Schmidt-Krey I. Two-dimensional crystallization by dialysis for structural studies of membrane proteins by the cryo-EM method electron crystallography. Meth Cell Biol 2013; 113: 325–337. CrossRef PubMed

Jun S., Zhao G., Ning J. et al. Correlative microscopy for 3D structural analysis of dynamic interactions. Journ Vis Exp 2013; 76: e50386.

Kim J.J. Using viral genomics to develop viral gene products as a novel class of drugs to treat human ailments. Biotech Lett 2001; 23(13): 1015–1020. CrossRef

Kiss G., Chen X., Brindley M.A. et al. Capturing enveloped viruses on affinity grids for downstream cryo-electron microscopy applications. Microsc Microanal 2014; 20(1): 164–174. CrossRef PubMed

Knoops K., Schoehn G., Schaffitzel C. Cryo-electron microscopy of ribosomal complexes in cotranslational folding, targeting, and translocation. Wil Interdisc Rev RNA 2012; 3(3): 429–441. CrossRef PubMed

Koning R.I., Koster A.J. Cellular nanoimaging by cryo electron tomography. Meth Mol Biol 2013; 950: 227–251.

Kucukelbir A., Sigworth F.J., Tagare H.D. Quantifying the local resolution of cryo-EM density maps. Nat Meth 2014; 11(1): 63–65. CrossRef PubMed

Kudryashev M., Stahlberg H., CastaÑo-Dнez D. Assessing the benefits of focal pair cryo-electron tomography. Journ Struct Biol 2012; 178(2): 88–97. CrossRef PubMed

Kwon S., Choi S.B., Park M.G. et al. Extraction of three-dimensional information of biological membranous tissue with scanning confocalinfrared laser microscope tomography. Micros Microanal 2013; 19 (Suppl 5): 194–197.

Kymionis G.D., Grentzelos M.A., Plaka A.D. et al. Correlation of the corneal collagen cross-linking demarcation line using confocal microscopy and anterior segment optical coherence tomography in keratoconic patients. Am Journ Ophthalmol 2014; 157(1): 110–115. CrossRef PubMed

Lagarde M., Géloën A., Record M. et al. Lipidomics is emerging. Biochim Biophys Acta 2003; 1634(3): 61. CrossRef PubMed

Lee J., Saha A., Pancera S.M. et al. Shear free and blotless cryo-TEM imaging: a new method for probing early evolution of nanostructures. Langmuir 2012; 28(9): 4043–4046. CrossRef PubMed

Leforestier A., Lemercier N., Livolant F. Contribution of cryoelectron microscopy of vitreous sections to the understanding of biological membrane structure. Proc Nat Acad Sci USA 2012; 109(23): 8959–8964. CrossRef PubMed

Lerch T.F., O'Donnell J.K., Meyer N.L. et al. Structure of AAV-DJ, a retargeted gene therapy vector: cryo-electron microscopy at 4.5Е resolution. Structure 2012; 20(8): 1310–1320. CrossRef PubMed

Li M., Zheng W. All-atom structural investigation of kinesin-microtubule complex constrained by high-quality cryo-electron-microscopy maps. Biochemistry 2012; 51(25): 5022–5032. CrossRef PubMed

Li X., Mooney P., Zheng S. et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Meth 2013; 10(6): 584–590. CrossRef PubMed

Lin J., Cheng N., Hogle J.M. et al. Conformational shift of a major poliovirus antigen confirmed by immuno-cryogenic electron microscopy. Journ Immunol 2013; 191(2): 884–891. CrossRef PubMed

LuÄiÄ V., Rigort A., Baumeister W. Cryo-electron tomography: the challenge of doing structural biology in situ. Journ Cell Biol 2013; 202(3): 407–419. CrossRef PubMed

Ludtke S.J., Lawson C.L., Kleywegt G.J. et al. The 2010 cryo-EM modeling challenge. Biopolymers 2012; 97(9): 651–654. CrossRef PubMed

Martinez J.M., Swan B.K., Wilson W.H. Marine viruses, a genetic reservoir revealed by targeted viromics. ISME Journ 2014; 8(5): 1079–1088. CrossRef PubMed

McCully M., Canny M. Quantitative cryo-analytical scanning electron microscopy (CEDX): an important technique useful for cell-specific localization of salt. Meth Mol Biol 2012; 913: 137–148.

Milne J.L., Borgnia M.J., Bartesaghi A. et al. Cryo-electron microscopy – a primer for the non-microscopist. FEBS Journ 2013; 280(1): 28–45. CrossRef PubMed

Miyazaki N., Nakagawa A., Iwasaki K. Life cycle of phyto-reoviruses visualized by electron microscopy and tomo-graphy. Front Microb 2013; 4(306): 1–9.

Müllertz A., Fatouros D.G., Smith J.R. et al. Insights into intermediate phases of human intestinal fluids visualized by atomic force microscopy and cryo-transmission electron microscopy ex vivo. Mol Pharm 2012; 9(2): 237–247. CrossRef PubMed

Nederlof I., Li Y.W., van Heel M., Abrahams J.P. Imaging protein three-dimensional nano-crystals with cryo-EM. Acta Crystallogr D: Biol. Crystallogr 2013; 69: 852–859. CrossRef PubMed

Nejadasl F.K., Karuppasamy M., Newman E.R. et al. Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images. Journ Synchrotron Radiat 2013; 20: 58–66. CrossRef PubMed

Noble A.J., Zhang Q., O'Donnell J. et al. A pseudoatomic model of the COPII cage obtained from cryo-electron microscopy and mass spectrometry. Nat Struct Mol Biol 2013; 20(2): 167–173. CrossRef PubMed

Norousi R., Wickles S., Leidig C. et al. Automatic post-picking using MAPPOS improves particle image detection from cryo-EM micrographs. Journ Struct Biol 2013; 182(2): 59–66. CrossRef PubMed

Nyuta K., Yoshimura T., Tsuchiya K. et al. Zwitterionic heterogemini surfactants containing ammonium and carboxylate headgroups 2: aggregation behavior studied by SANS, DLS, and cryo-TEM. Journ Colloid Interface Sci 2012; 370(1): 80–85. CrossRef PubMed

Oda T., Kikkawa M. Novel structural labeling method using cryo-electron tomography and biotin-streptavidin system. Journ Struc Biol 2013; 183(3): 305–311. CrossRef PubMed

Ounjai P., Kim K.D., Lishko P.V., Downing K.H. Three-dimensional structure of the bovine sperm connecting piece revealed by electron cryotomography. Biol Reprod 2012; 87(3): 1–9. CrossRef PubMed

Paessens L.C., Fluitsma D.M., van Kooyk Y. Haematopoietic antigen-presenting cells in the human thymic cortex: evidence for a role in selection and removal of apoptotic thymocytes. Journ Pathol 2008; 214(1): 96–103. CrossRef PubMed

Pandurangan A.P., Topf M. RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps. Bioinformatics 2012; 28(18): 2391–2393. CrossRef PubMed

Pigino G., Cantele F., Vannuccini E. et al. Electron tomography of IFT particles. Meth Enzymol 2013; 524: 325–342. CrossRef PubMed

Quan B.D., Sone E.D. Cryo-TEM analysis of collagen fibrillar structure. Meth Enzymol 2013; 532: 189–205. CrossRef PubMed

Rigort A., Bäuerlein F.J., Villa E. et al. Focused ion beam micro-machining of eukaryotic cells for cryoelectron tomography. Proc Nat Acad Sci USA 2012; 109(12): 4449–4454. CrossRef PubMed

Rigort A., Villa E., Bäuerlein F.J. et al. Integrative approaches for cellular cryo-electron tomography: correlative imaging and focused ion beam micromachining. Meth Cell Biol 2012; 111: 259–281. CrossRef PubMed

Rusu M., Wriggers W. Evolutionary bidirectional expansion for the tracing of alpha helices in cryo-electron microscopy reconstructions. Journ Struc Biol 2012; 177(2): 410–419. CrossRef PubMed

Schellenberger P., Kaufmann R., Siebert C.A. et al. High-precision correlative fluorescence and electron cryo-microscopy using two independent alignment markers. Ultramicroscopy 2014; 143: 41–51. CrossRef PubMed

Scheres S.H. A Bayesian view on cryo-EM structure determination. Journ Mol Biol 2012; 415(2): 406–418. CrossRef PubMed

Schertel A., Snaidero N., Han H.M. et al. Cryo FIB-SEM: Volume imaging of cellular ultra-structure in native frozen specimens. Journ Struc Biol 2013; 184(2): 355–360. CrossRef PubMed

Schorb M., Briggs J.A. Correlated cryo-fluorescence and cryo-electron microscopy with high spatial precision and improved sensitivity. Ultramicroscopy 2014; 143: 24–32. CrossRef PubMed

Shang Z., Sigworth F.J. Hydration-layer models for cryo-EM image simulation. Journ Struct Biol 2012; 180(1): 10–16. CrossRef PubMed

Sharp T.H., Bruning M., Mantell J. et al. Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design. Proc Nat Acad Sci USA 2012; 109(33): 13266–13271. CrossRef PubMed

Shigematsu H., Sigworth F.J. Noise models and cryo-EM drift correction with a direct-electron camera. Ultramicroscopy 2013; 131: 61–69. CrossRef PubMed

Shimanouchi T., Oyama E., Ishii H. et al. Membranomics research on interactions between liposome membranes with membrane chip analysis. Membrane 2009; 34(6): 342–350. CrossRef

Shrum D.C., Woodruff B.W., Stagg S.M. Creating an infra-structure for high-throughput high-resolution cryogenic electron microscopy. Journ Struc Biol 2012; 180(1): 254–258. CrossRef PubMed

Si D., Ji S., Nasr K.A., He J. A machine learning approach for the identification of protein secondary structure elements from electron cryo-microscopy density maps. Biopolymers 2012; 97(9): 698–708. CrossRef PubMed

Singer A., Zhao Z., Shkolnisky Y., Hadani R. Viewing angle classification of cryo-electron microscopy images using eigenvectors. SIAM Journ Imaging Sci 2011; 4(2): 723–759. CrossRef PubMed

Song K., Comolli L.R., Horowitz M. Removing high contrast artifacts via digital inpainting in cryo-electron tomography: an application of compressed sensing. Journ Struc Biol 2012; 178(2): 108–120. CrossRef PubMed

Strunk K.M., Wang K., Ke D. et al. Thinning of large mammalian cells for cryo-TEM characterization by cryo-FIB milling. Journ Microsc 2012; 247(3): 220–227. CrossRef PubMed

Sun J., Kawakami H., Zech J. et al. Cdc6-induced conformational changes in ORC bound to origin DNA revealed by cryo-electron microscopy. Structure 2012; 20(3): 534–544. CrossRef PubMed

Tatischeff I., Larquet E., Falcón-Pérez J.M. et al. Fast characterisation of cell-derived extracellular vesicles by nanoparticles tracking analysis, cryo-electron microscopy, and Raman tweezers microspectroscopy. Journ Extracell Vesicles 2012: 1–11.

Taylor K.A., Glaeser R.M. Retrospective on the early development of cryoelectron microscopy of macromolecules and a prospective on opportunities for the future. Journ Struc Biol 2008; 163(3): 214–223. CrossRef PubMed

Tremoulet A.H., Albani S. Immunomics in clinical development: bridging the gap. Exp Rev Clin Immunol 2005; 1(1): 3–6. CrossRef PubMed

Vahedi-Faridi A., Jastrzebska B., Palczewski K., Engel A. 3D imaging and quantitative analysis of small solubilized membrane proteins and their complexes by transmission electron microscopy. Microscopy 2013; 62(1): 95–107. CrossRef PubMed

Vargas J., Otуn J., Marabini R. et al. FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy. Journ Struc Biol 2013; 181(2): 136–148. CrossRef PubMed

Vonesch C., Wang L., Shkolnisky Y., Singer A. Fast wavelet-based single-particle reconstruction in cryo-EM. Proceedings of the 8th IEEE Int Symp on Biomed. Imaging: From Nano to Macro; 2011; Chicago, Illinois. p. 1950–1953.

VuloviÄ M., Ravelli R.B., van Vliet L.J. et al. Image formation modeling in cryo-electron microscopy. Journ Struct Biol 2013; 183(1): 19–32. CrossRef PubMed

Walter A., Muzik H., Vieker H. et al. Practical aspects of Boersch phase contrast electron microscopy of biological specimens. Ultramicroscopy 2012; 116: 62–72. CrossRef PubMed

Wang J., Yin C. A Zernike-moment-based non-local denoising filter for cryo-EM images. Sci Ch Life Sci 2013; 56(4): 384–390. CrossRef PubMed

Wang K., Strunk K., Zhao G. et al. 3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography. Journ Struc Biol 2012; 180(2): 318–326. CrossRef PubMed

Wang Q., Matsui T., Domitrovic T. et al. Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps. Journ Struc Biol 2013; 181(3): 195–206. CrossRef PubMed

Wang Z., Gao K., Chen J. et al. Advantages of intermediate X-ray energies in Zernike phase contrast X-ray microscopy. Biotech Adv 2013; 31(3): 387–392. CrossRef PubMed

Weber M., Huisken J. Omnidirectional microscopy. Nat Meth 2012; 9: 656–657. CrossRef PubMed

Weiner A., Kapishnikov S., Shimoni E. et al. Vitrification of thick samples for soft X-ray cryo-tomography by high pressure freezing. Journ Struc Biol 2013; 181(1): 77–81. CrossRef PubMed

Willmann J., Leibfritz D., Thiele H. Hyphenated tools for phospholipidomics. Journ Biomol Tech 2008; 19(3): 211–216.

Yajima H., Ogura T., Nitta R. et al. Conformational changes in tubulin in GMPCPP and GDP-taxol microtubules observed by cryoelectron microscopy. Journ Cell Biol 2012; 198(3): 315–322. CrossRef PubMed

Yang F., Abe K., Tani K., Fujiyoshi Y. Carbon sandwich preparation preserves quality of two-dimensional crystals for cryo-electron microscopy. Microscopy 2013; 62(6): 597–606. CrossRefPubMed

Yoder J.D., Cifuente J.O., Pan J. et al. The crystal structure of a coxsackievirus B3–RD variant and a refined 9-angstrom cryo-electron microscopy reconstruction of the virus com-plexed with decay-accelerating factor (DAF) provide a new footprint of DAF on the virus surface. Journ Virol 2012; 86(23): 12571–12581. CrossRef PubMed

Zhang L., Tong H., Garewal M., Ren G. Optimized negative-staining electron microscopy for lipoprotein studies. Biochim Biophys Acta 2013; 1830(1): 2150–2159. CrossRef PubMed

Zhang P. Correlative cryo-electron tomography and optical microscopy of cells. Curr Opin Struc Biol 2013; 23(5): 763–770. CrossRef PubMed

Zhang X., Ge P., Yu X. et al. Cryo-EM structure of the mature dengue virus at 3.5–A resolution. Nat Struc Mol Biol 2013; 20(1): 105–110. CrossRef PubMed

Zhao G., Perilla J.R., Yufenyuy E.L. et al. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature 2013; 497(7451): 643–646. CrossRef PubMed

Zou X., Hovmöller S., Oleynikov P. Phase contrast, contrast transfer function (CTF) and high-resolution electron microscopy (HRTEM). In: Electron Crystallography: Electron Microscopy and Electron Diffraction. Oxford, New York 2011: 131–155.

Zuckerkandl E., Pauling L. Molecules as documents of evolutionary history. Journ Theor Biol 1965; 8(2): 357–366. CrossRef

Опубліковано

2014-09-15

Як цитувати

Gradov, O. V., & Gradova, M. A. (2014). Криоэлектронная микроскопия как инструмент системной биологии, структурного анализа и экспериментального воздействия на клетки. Комплексный аналитический обзор новейших работ. Проблеми кріобіології і кріомедицини, 24(3), 193–211. https://doi.org/10.15407/cryo24.03.193