SEMC Publications2018-07-20T15:34:18+00:00

SEMC Publications

2018

Alphonse S, Ghose R. wwwwMethyl NMR Spectroscopy: Measurement of Dynamics in Viral RNA-directed RNA Polymerases. Methods. 2018. Link

Benoit M, Asenjo AB, Sosa H. Cryo-EM reveals the structural basis of microtubule depolymerization by kinesin-13s. Nat Commun. 2018;9(1):1662. PMCID: PMC5916938. Link

Bepler T, Morin A, Noble AJ, Brasch J, Shapiro L, Berger B. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Res Comput Mol Biol. 2018;10812:245-7. PMCID: PMC5917602. Link

Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA. Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts. eLife. 2018;7. PMCID: PMC5837556. Link

Cao S, Zhou K, Zhang Z, Luger K, Straight AF. Constitutive centromere-associated network contacts confer differential stability on CENP-A nucleosomes in vitro and in the cell. Molecular biology of the cell. 2018;29(6):751-62. Link

Cheng A, Eng ET, Alink L, Rice WJ, Jordan KD, Kim LY, Potter CS, Carraggher B. High Resolution Single Particle Cryo-Electron Microscopy using Beam-Image Shift. bioRxiv. 2018. Link

Dandey VP, Wei H, Zhang Z, Tan YZ, Acharya P, Eng ET, Rice WJ, Kahn PA, Potter CS, Carragher B. Spotiton: New features and applications. Journal of structural biology. 2018;202(2):161-9.  Link

Dingens AS, Acharya P, Haddox HK, Rawi R, Xu K, Chuang G-Y, Wei H, Mascola JR, Carragher B, Potter CS, Overbaugh J, Kwong PD, Bloom JD. Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV. bioRxiv. 2018. Link

Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina TV, Artsimovitch I, Landick R, Darst SA. Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators. Cell. 2018.Link

Kim LY, Carragher B, Rice WJ, Eng ET, Kopylov M, Cheng A, Raczkowski AM, Jordan KD, Bobe D, Potter C. Benchmarking cryo-EM single particle analysis workflow. bioRxiv. 2018. Link

Liao PC, Boldogh IR, Siegmund SE, Freyberg Z, Pon LA. Isolation of mitochondria from Saccharomyces cerevisiae using magnetic bead affinity purification. PloS one. 2018;13(4):e0196632. PMCID: PMC5919621. Link

Lin W, Das K, Degen D, Mazumder A, Duchi D, Wang D, Ebright YW, Ebright RY, Sineva E, Gigliotti M, Srivastava A, Mandal S, Jiang Y, Liu Y, Yin R, Zhang Z, Eng ET, Thomas D, Donadio S, Zhang H, Zhang C, Kapanidis AN, Ebright RH. Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3). Molecular cell. 2018;70(1):60-71 e15. Link

Lopez-Redondo ML, Coudray N, Zhang Z, Alexopoulos J, Stokes DL. Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(12):3042-7. PMCID: PMC5866550. Link

Ma X, Lu M, Gorman J, Terry DS, Hong X, Zhou Z, Zhao H, Altman RB, Arthos J, Blanchard SC, Kwong PD, Munro JB, Mothes W. HIV-1 Env trimer opens through an asymmetric intermediate in which individual protomers adopt distinct conformations. eLife. 2018;7. PMCID: PMC5896952. Link

Malvezzi M, Andra KK, Pandey K, Lee BC, Falzone ME, Brown A, Iqbal R, Menon AK, Accardi A. Out-of-the-groove transport of lipids by TMEM16 and GPCR scramblases. Proceedings of the National Academy of Sciences of the United States of America. 2018. Link

McGoldrick LL, Singh AK, Saotome K, Yelshanskaya MV, Twomey EC, Grassucci RA, Sobolevsky AI. Opening of the human epithelial calcium channel TRPV6. Nature. 2018;553(7687):233-7. PMCID: PMC5854407. Link

Niekamp S, Coudray N, Zhang N, Vale RD, Bhabha G. Stalk-mediated communication in the dynein motor domain. bioRxiv. 2018. Link

Noble AJ, Dandey VP, Wei H, Brasch J, Chase J, Acharya P, Tan YZ, Zhang Z, Kim LY, Scapin G, Rapp M, Eng ET, Rice WJ, Cheng A, Negro CJ, Shapiro L, Kwong PD, Jeruzalmi D, des Georges A, Potter CS, Carragher B. Routine single particle CryoEM sample and grid characterization by tomography. eLife. 2018;7. Link

Noble AJ, Wei H, Dandey VP, Zhang Z, Potter CS, Carragher B. Reducing effects of particle adsorption to the air-water interface in cryoEM. bioRxiv. 2018. Link

Oliveira LM, Ye Z, Katz A, Alimova A, Wei H, Herman GT, Gottlieb P. Component tree analysis of cystovirus phi6 nucleocapsid Cryo-EM single particle reconstructions. PloS one. 2018;13(1):e0188858. PMCID: PMC5754084.Link

Pisareva VP, Pisarev AV, Fernandez IS. Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES. eLife. 2018;7. PMCID: PMC5984033. Link

Rice WJ, Cheng A, Noble AJ, Eng ET, Kim LY, Carragher B, Potter CS. Routine Determination of Ice Thickness for Cryo-EM Grids. bioRxiv. 2018. Link

Scapin G, Dandey VP, Zhang Z, Prosise W, Hruza A, Kelly T, Mayhood T, Strickland C, Potter CS, Carragher B. Structure of the insulin receptor-insulin complex by single-particle cryo-EM analysis. Nature. 2018;556(7699):122-5. PMCID: PMC5886813.Link

Schmidpeter PAM, Gao X, Uphadyay V, Rheinberger J, Nimigean CM. Ligand binding and activation properties of the purified bacterial cyclic nucleotide-gated channel SthK. J Gen Physiol. 2018;150(6):821-34. PMCID: PMC5987880. Link

Sun C, Benlekbir S, Venkatakrishnan P, Wang Y, Hong S, Hosler J, Tajkhorshid E, Rubinstein JL, Gennis RB. Structure of the alternative complex III in a supercomplex with cytochrome oxidase. Nature. 2018. Link

Sun Y, Zhang Y, Hamilton K, Manley JL, Shi Y, Walz T, Tong L. Molecular basis for the recognition of the human AAUAAA polyadenylation signal. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(7):E1419-E28. PMCID: PMC5816196. Link

Tan YZ, Aiyer S, Mietzsch M, Hull JA, McKenna R, Grieger J, Samulski RJ, Baker TS, Agbandje-McKenna M, Lyumkis D. Sub-2 Å Ewald Curvature Corrected Single-Particle Cryo-EM. bioRxiv. 2018.Link

Wei H, Dandey VP, Zhang Z, Raczkowski A, Rice WJ, Carragher B, Potter CS. Optimizing “self-wicking” nanowire grids. Journal of structural biology. 2018;202(2):170-4. PMCID: PMC5864531. Link

Weick EM, Puno MR, Januszyk K, Zinder JC, DiMattia MA, Lima CD. Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex. Cell. 2018;173(7):1663-77 e21. Link

Xu K, Acharya P, Kong R, Cheng C, Chuang GY, Liu K, Louder MK, O’Dell S, Rawi R, Sastry M, Shen CH, Zhang B, Zhou T, Asokan M, Bailer RT, Chambers M, Chen X, Choi CW, Dandey VP, Doria-Rose NA, Druz A, Eng ET, Farney SK, Foulds KE, Geng H, Georgiev IS, Gorman J, Hill KR, Jafari AJ, Kwon YD, Lai YT, Lemmin T, McKee K, Ohr TY, Ou L, Peng D, Rowshan AP, Sheng Z, Todd JP, Tsybovsky Y, Viox EG, Wang Y, Wei H, Yang Y, Zhou AF, Chen R, Yang L, Scorpio DG, McDermott AB, Shapiro L, Carragher B, Potter CS, Mascola JR, Kwong PD. Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1. Nat Med. 2018;24(6):857-67. Link

Zhang Z, Liang WG, Bailey LJ, Tan YZ, Wei H, Wang A, Farcasanu M, Woods VA, McCord LA, Lee D, Shang W, Deprez-Poulain R, Deprez B, Liu DR, Koide A, Koide S, Kossiakoff AA, Li S, Carragher B, Potter CS, Tang WJ. Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme. eLife. 2018;7. Link

2017

Alewijnse, B., A.W. Ashton, M.G. Chambers, S. Chen, A. Cheng, M. Ebrahim, E.T. Eng, W.J.H. Hagen, A.J. Koster, C.S. Lopez, N. Lukoyanova, J. Ortega, L. Renault, S. Reyntjens, W.J. Rice, G. Scapin, R. Schrijver, A. Siebert, S.M. Stagg, V. Grum-Tokars, E.R. Wright, S. Wu, Z. Yu, Z.H. Zhou, B. Carragher, and C.S. Potter. Best practices for managing large CryoEM facilities. J Struct Biol. 199:225-236. PubMed PMID PMC5605453. Link

Baldwin, P.R., Y.Z. Tan, E.T. Eng, W.J. Rice, A.J. Noble, C.J. Negro, M.A. Cianfrocco, C.S. Potter, and B. Carragher. 2017. Big data in cryoEM: automated collection, processing and accessibility of EM data. Current opinion in microbiology. 43:1-8. PubMed PMID 29100109 Link

Campos, M.P., M.P. Hendricks, A.N. Beecher, W. Walravens, R.A. Swain, G.T. Cleveland, Z. Hens, M.Y. Sfeir, and J.S. Owen. 2017. A Library of Selenourea Precursors to PbSe Nanocrystals with Size Distributions near the Homogeneous Limit. Journal of the American Chemical Society. 139:2296-2305. PubMed PCID 28103035. Link

Coleman, R.A., Z. Qiao, S.K. Singh, C.S. Peng, M. Cianfrocco, Z. Zhang, A. Piasecka, H. Aldeborgh, G. Basishvili, and W.L. Liu. 2017. p53 Dynamically Directs TFIID Assembly on Target Gene Promoters. Molecular and cellular biology. 37. PubMed PMID:28416636. Link

Guo, H., S.A. Bueler, and J.L. Rubinstein. 2017a. Atomic model for the dimeric FO region of mitochondrial ATP synthase. Science. PubMed PMID: 29074581. Link

Guo, T.W., A. Bartesaghi, H. Yang, V. Falconieri, P. Rao, A. Merk, E.T. Eng, A.M. Raczkowski, T. Fox, L.A. Earl, D.J. Patel, and S. Subramaniam. 2017b. Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex. Cell. 171:414-426 e412. PubMed PMID: 28985564. Link

Hirabayashi, Y., S.K. Kwon, H. Paek, W.M. Pernice, M.A. Paul, J. Lee, P. Erfani, A. Raczkowski, D.S. Petrey, L.A. Pon, and F. Polleux. 2017. ER-mitochondria tethering by PDZD8 regulates Ca2+ dynamics in mammalian neurons. Science. 358:623-630. PubMed PMID: 29097544. Link

Silva, M., N. Morsci, K.C.Q. Nguyen, A. Rizvi, C. Rongo, D.H. Hall, and M.M. Barr. 2017. Cell-Specific alpha-Tubulin Isotype Regulates Ciliary Microtubule Ultrastructure, Intraflagellar Transport, and Extracellular Vesicle Biology. Current biology : CB. 27:968-980. PubMed PMCID: PMC5688951. Link

Tan, Y.Z., P.R. Baldwin, J.H. Davis, J.R. Williamson, C.S. Potter, B. Carragher, and D. Lyumkis. 2017. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat Methods. 14:793-796. PubMed PMCID: PMC5533649 . Link

Malyutin, A.G., Musalgaonkar, S., Patchett, S., Frank, J., and Johnson, A.W. (2017). Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis. EMBO J 36, 854-868. PMID: 28179369; PMCid: PMC5376978. .Link

Chowdhury S, Carter J, Rollins MF, Golden SM, Jackson RN, Hoffmann C, et al. Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex. Cell. 2017;169(1):47-57 e11. doi: 10.1016/j.cell.2017.03.012. PubMed PMID: 28340349. Link

James ZM, Borst AJ, Haitin Y, Frenz B, DiMaio F, Zagotta WN, et al. CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel. Proc Natl Acad Sci U S A. 2017;114(17):4430-5. doi: 10.1073/pnas.1700248114. PubMed PMID: 28396445. Link

Liu Q, Acharya P, Dolan MA, Zhang P, Guzzo C, Lu J, et al. Quaternary contact in the initial interaction of CD4 with the HIV-1 envelope trimer. Nat Struct Mol Biol. 2017;24(4):370-8. doi: 10.1038/nsmb.3382. PubMed PMID: 28218750. Link

Ren Y, Schmiege P, Blobel G. Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1. Elife. 2017;6. doi: 10.7554/eLife.20070. PubMed PMID: 28059701; PubMed Central PMCID: PMCPMC5218534. Link

Scapin G, Prosise WW, Wismer MK, Strickland C. A novel storage system for cryoEM samples. Journal of structural biology. 2017. doi: 10.1016/j.jsb.2017.04.005. PubMed PMID: 28433496. Link

Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, et al. Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. Structure. 2017;25(3):434-45. doi: 10.1016/j.str.2017.01.006. PubMed PMID: 28162953; PubMed Central PMCID: PMCPMC5342941. Link

Wang L, Eng ET, Law K, Gordon RE, Rice WJ, Chen BK. Visualization of HIV T Cell Virological Synapses and Virus-Containing Compartments by Three-Dimensional Correlative Light and Electron Microscopy. J Virol. 2017;91(2). doi: 10.1128/JVI.01605-16. PubMed PMID: 27847357; PubMed Central PMCID: PMCPMC5215336. Link

Yuan Z, Riera A, Bai L, Sun J, Nandi S, Spanos C, et al. Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1. Nat Struct Mol Biol. 2017;24(3):316-24. doi: 10.1038/nsmb.3372. PubMed PMID: 28191893. Link

2016

Tan YZ, Cheng A, Potter CS, Carragher B. Automated data collection in single particle electron microscopy. Microscopy (Oxf). 2016;65(1):43-56. doi: 10.1093/jmicro/dfv369. PubMed PMID: 26671944; PubMed Central PMCID: PMCPMC4749047. Link

Singhvi A, Liu B, Friedman CJ, Fong J, Lu Y, Huang XY, et al. A Glial K/Cl Transporter Controls Neuronal Receptive Ending Shape by Chloride Inhibition of an rGC. Cell. 2016;165(4):936-48. doi: 10.1016/j.cell.2016.03.026. PubMed PMID: 27062922; PubMed Central PMCID: PMCPMC4860081. Link

Singh RK, Barbosa-Lorenzi VC, Lund FW, Grosheva I, Maxfield FR, Haka AS. Degradation of aggregated LDL occurs in complex extracellular sub-compartments of the lysosomal synapse. J Cell Sci. 2016;129(5):1072-82. doi: 10.1242/jcs.181743. PubMed PMID: 26801085; PubMed Central PMCID: PMCPMC4813320. Link

Razinkov I, Dandey VP, Wei H, Zhang Z, Melnekoff D, Rice WJ, et al. A new method for vitrifying samples for cryoEM. Journal of structural biology. 2016;195(2):190-8. doi: 10.1016/j.jsb.2016.06.001. PubMed PMID: 27288865. Link

Peng X, Yuan X-Z, Somasundaran P, Patra P. Assessment of micro-polarity anisotropy as a function of surfactant packing in sodium dodecyl sulphonate-hexane reverse micelles. Soft Matter. 2016;12(1):22-5. doi: 10.1039/C5SM01950H. PubMed PMID: 26446876. Link

Leo-Macias A, Agullo-Pascual E, Sanchez-Alonso JL, Keegan S, Lin X, Arcos T, et al. Nanoscale visualization of functional adhesion/excitability nodes at the intercalated disc. Nat Commun. 2016;7:10342. doi: 10.1038/ncomms10342. PubMed PMID: 26787348; PubMed Central PMCID: PMCPMC4735805. Link

Haka AS, Barbosa-Lorenzi VC, Lee HJ, Falcone DJ, Hudis CA, Dannenberg AJ, et al. Exocytosis of macrophage lysosomes leads to digestion of apoptotic adipocytes and foam cell formation. J Lipid Res. 2016;57(6):980-92. doi: 10.1194/jlr.M064089. PubMed PMID: 27044658; PubMed Central PMCID: PMCPMC4878183. Link

Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, et al. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell. 2016;167(5):1215-28 e25. doi: 10.1016/j.cell.2016.10.028. PubMed PMID: 27839866; PubMed Central PMCID: PMC5130164. Link

Domanski M, Upla P, Rice WJ, Molloy KR, Ketaren NE, Stokes DL, et al. Purification and analysis of endogenous human RNA exosome complexes. Rna. 2016;22(9):1467-75. doi: 10.1261/rna.057760.116. PubMed PMID: 27402899; PubMed Central PMCID: PMC4986900. Link

Davis JH, Tan YZ, Carragher B, Potter CS, Lyumkis D, Williamson JR. Modular Assembly of the Bacterial Large Ribosomal Subunit. Cell. 2016;167(6):1610-22 e15. doi: 10.1016/j.cell.2016.11.020. PubMed PMID: 27912064; PubMed Central PMCID: PMCPMC5145266. Link

Cheng A, Tan YZ, Dandey VP, Potter CS, Carragher B. Strategies for Automated CryoEM Data Collection Using Direct Detectors. Methods Enzymol. 2016;579:87-102. doi: 10.1016/bs.mie.2016.04.008. PubMed PMID: 27572724. Link

2015

Totland C, Martinez-Santiago J, Ananthapadmanabhan KP, Somasundaran P. Composition and structural transitions of polyelectrolyte-surfactant complexes in the presence of fatty acid studied by NMR and cryo-SEM. Langmuir : the ACS journal of surfaces and colloids. 2015;31(5):1623-31. doi: 10.1021/la504181a. PubMed PMID: 25590530. Link

Neel BA, Zong H, Backer JM, Pessin JE. Identification of Atypical Peri-Nuclear Multivesicular Bodies in Oxidative and Glycolytic Skeletal Muscle of Aged and Pompe’s Disease Mouse Models. Frontiers in physiology. 2015;6:393. Epub 2016/01/07. doi: 10.3389/fphys.2015.00393. PubMed PMID: 26733885; PubMed Central PMCID: PMCPMC4685069. Link

Leo-Macias A, Liang FX, Delmar M. Ultrastructure of the intercellular space in adult murine ventricle revealed by quantitative tomographic electron microscopy. Cardiovasc Res. 2015;107(4):442-52. doi: 10.1093/cvr/cvv182. PubMed PMID: 26113266; PubMed Central PMCID: PMCPMC4540145. Link

Lasala R, Coudray N, Abdine A, Zhang Z, Lopez-Redondo M, Kirshenbaum R, et al. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Journal of structural biology. 2015;189(2):123-34. doi: 10.1016/j.jsb.2014.11.008. PubMed PMID: 25478971; PubMed Central PMCID: PMCPMC4419781. Link

Kang Y, Zhou XE, Gao X, He Y, Liu W, Ishchenko A, et al. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature. 2015;523(7562):561-7. doi: 10.1038/nature14656. PubMed PMID: 26200343; PubMed Central PMCID: PMCPMC4521999. Link

Hurd TR, Sanchez CG, Teixeira FK, Petzold C, Dancel-Manning K, Wang JY, et al. Ultrastructural Analysis of Drosophila Ovaries by Electron Microscopy. Methods Mol Biol. 2015;1328:151-62. doi: 10.1007/978-1-4939-2851-4_11. PubMed PMID: 26324436; PubMed Central PMCID: PMCPMC4727969. Link

Hsu YC, Chuang JZ, Sung CH. Light regulates the ciliary protein transport and outer segment disc renewal of mammalian photoreceptors. Developmental cell. 2015;32(6):731-42. doi: 10.1016/j.devcel.2015.01.027. PubMed PMID: 25805137; PubMed Central PMCID: PMCPMC4374123. Link

Hall DH, Rice WJ. Electron Tomography Methods for C. elegans. Methods Mol Biol. 2015;1327:141-58. doi: 10.1007/978-1-4939-2842-2_11. PubMed PMID: 26423973. Link

Chuang JZ, Hsu YC, Sung CH. Ultrastructural visualization of trans-ciliary rhodopsin cargoes in mammalian rods. Cilia. 2015;4:4. doi: 10.1186/s13630-015-0013-1. PubMed PMID: 25664179; PubMed Central PMCID: PMCPMC4320831. Link

Correction for Kaushal et al., Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. Proc Natl Acad Sci U S A. 2015;112(20):E2736. doi: 10.1073/pnas.1507224112. PubMed PMID: 25922530; PubMed Central PMCID: PMCPMC4443313. Link