Ward AB, Sali A, Wilson IA. Integrative structural biology. Science. 2013; 339(6122):913–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Graewert MA, Svergun DI. Impact and progress in small and wide angle x-ray scattering (saxs and waxs). Curr Opin Struct Biol. 2013; 23(5):748–54.
Article
CAS
PubMed
Google Scholar
Kikhney AG, Svergun DI. A practical guide to small angle x-ray scattering (saxs) of flexible and intrinsically disordered proteins. FEBS Lett. 2015; 589(19):2570–7.
Article
CAS
PubMed
Google Scholar
Putnam CD, Hammel M, Hura GL, Tainer JA. X-ray solution scattering (saxs) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys. 2007; 40(03):191–285.
Article
CAS
PubMed
Google Scholar
Jacques DA, Trewhella J. Small angle scattering for structural biology expanding the frontier while avoiding the pitfalls. Protein Sci. 2010; 19(4):642–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Konarev PV, Svergun DI. A posteriori determination of the useful data range for small-angle scattering experiments on dilute monodisperse systems. IUCrJ. 2015; 2(3):352–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Semenyuk A, Svergun D. Gnom–a program package for small-angle scattering data processing. J Appl Crystallogr. 1991; 24(5):537–40.
Article
Google Scholar
Bergmann A, Fritz G, Glatter O. Solving the generalized indirect fourier transformation (gift) by boltzmann simplex simulated annealing (bssa). J Appl Crystallogr. 2000; 33(5):1212–6.
Article
CAS
Google Scholar
Petoukhov MV, Svergun DI. Ambiguity assessment of small-angle scattering curves from monodisperse systems. Biol Crystallogr. 2015; 71(5):1051–8.
Article
CAS
Google Scholar
Kuwamoto S, Akiyama S, Fujisawa T. Radiation damage to a protein solution, detected by synchrotron X-ray small-angle scattering: dose-related considerations and suppression by cryoprotectants. J Synchrotron Radiat. 2004; 11(6):462–8.
Article
CAS
PubMed
Google Scholar
Jeffries CM, Graewert MA, Svergun DI, Blanchet CE. Limiting radiation damage for high-brilliance biological solution scattering: practical experience at the embl p12 beamline petraiii. J Synchrotron Radiat. 2015; 22(2):273–9.
Article
CAS
PubMed
Google Scholar
Meisburger SP, Warkentin M, Chen H, Hopkins JB, Gillilan RE, Pollack L, Thorne RE. Breaking the radiation damage limit with cryo-saxs. Biophys J. 2013; 104(1):227–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Binnig G, Quate CF, Gerber C. Atomic force microscope. Phys Rev Lett. 1986; 56(9):930.
Article
PubMed
Google Scholar
Parot P, Dufrêne YF, Hinterdorfer P, Le Grimellec C, Navajas D, Pellequer JL, Scheuring S. Past, present and future of atomic force microscopy in life sciences and medicine. J Mol Recognit. 2007; 20(6):418–31.
Article
CAS
PubMed
Google Scholar
Engel A, Müller DJ. Observing single biomolecules at work with the atomic force microscope. Nat Struct MolBiol. 2000; 7(9):715–8.
Article
CAS
Google Scholar
Fotiadis D, Scheuring S, Müller SA, Engel A, Müller DJ. Imaging and manipulation of biological structures with the afm. Micron. 2002; 33(4):385–97.
Article
CAS
PubMed
Google Scholar
Costa L, Rodrigues MS, Newman E, Zubieta C, Chevrier J, Comin F. Imaging material properties of biological samples with a force feedback microscope. J Mol Recognit. 2013; 26(12):689–93.
Article
CAS
PubMed
Google Scholar
Schabert FA, Engel A. Reproducible acquisition of escherichia coli porin surface topographs by atomic force microscopy. Biophys J. 1994; 67(6):2394.
Article
CAS
PubMed
PubMed Central
Google Scholar
Scheuring S, Ringler P, Borgnia M, Stahlberg H, Müller DJ, Agre P, Engel A. High resolution afm topographs of the escherichia coli water channel aquaporin z. EMBO J. 1999; 18(18):4981–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chaves RC, Dahmane S, Odorico M, Nicolaes GA, Pellequer JL. Factor va alternative conformation reconstruction using atomic force microscopy. Thromb Haemost. 2014; 112(6):1167–73.
Article
CAS
PubMed
Google Scholar
Chen S-WW, Teulon JM, Godon C, Pellequer JL. Atomic force microscope, molecular imaging, and analysis. J Mol Recognit. 2016; 29(1):51–5.
Article
CAS
PubMed
Google Scholar
Hansma H, Vesenka J, Siegerist C, Kelderman G, Morrett H, Sinsheimer R, Elings V, Bustamante C, Hansma P. Reproducible imaging and dissection of plasmid dna under liquid with the atomic force microscope. Science. 1992; 256(5060):1180–4.
Article
CAS
PubMed
Google Scholar
Hong DP, Fink AL, Uversky VN. Structural characteristics of α-synuclein oligomers stabilized by the flavonoid baicalein. J Mol Biol. 2008; 383(1):214–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baldock C, Oberhauser AF, Ma L, Lammie D, Siegler V, Mithieux SM, Tu Y, Chow JYH, Suleman F, Malfois M, et al. Shape of tropoelastin, the highly extensible protein that controls human tissue elasticity. Proc Natl Acad Sci USA. 2011; 108(11):4322–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sander B, Tria G, Shkumatov AV, Kim EY, Grossmann JG, Tessmer I, Svergun DI, Schindelin H. Structural characterization of gephyrin by afm and saxs reveals a mixture of compact and extended states. Acta Crystallogr D Biol Crystallogr. 2013; 69(10):2050–60.
Article
CAS
PubMed
Google Scholar
Wu W, Huang J, Jia S, Kowalewski T, Matyjaszewski K, Pakula T, Gitsas A, Floudas G. Self-assembly of podma-b-pt ba-b-podma triblock copolymers in bulk and on surfaces. a quantitative saxs/afm comparison. Langmuir. 2005; 21(21):9721–7.
Article
CAS
PubMed
Google Scholar
Brus J, Špírková M, Hlavatá D, Strachota A. Self-organization, structure, dynamic properties, and surface morphology of silicaepoxy films as seen by solid-state nmr, saxs, and afm. Macromolecules. 2004; 37(4):1346–57.
Article
CAS
Google Scholar
Cheong CG, Eom SH, Chang C, Shin DH, Song HK, Min K, Moon JH, Kim KK, Hwang KY, Suh SW. Crystallization, molecular replacement solution, and refinement of tetrameric β-amylase from sweet potato. Proteins Struct Funct Bioinforma. 1995; 21(2):105–17.
Article
CAS
Google Scholar
Takeda Y, Hizukuri S. Improved method for crystallization of sweet potato beta-amylase. Biochim Biophys Acta. 1969; 185(2):469–71.
Article
CAS
PubMed
Google Scholar
Namba K, Stubbs G. Structure of tobacco mosaic virus at 3.6 a resolution: implications for assembly. Science. 1986; 231(4744):1401–6.
Article
CAS
PubMed
Google Scholar
Zenhausern F, Adrian M, Emch R, Taborelli M, Jobin M, Descouts P. Scanning force microscopy and cryo-electron microscopy of tobacco mosaic virus as a test specimen. Ultramicroscopy. 1992; 42:1168–72.
Article
PubMed
Google Scholar
Drygin YF, Bordunova OA, Gallyamov MO, Yaminsky IV. Atomic force microscopy examination of tobacco mosaic virus and virion rna. FEBS Lett. 1998; 425(2):217–21.
Article
CAS
PubMed
Google Scholar
Gebhardt R, Teulon JM, Pellequer JL, Burghammer M, Colletier JP, Riekel C. Virus particle assembly into crystalline domains enabled by the coffee ring effect. Soft Matter. 2014; 10(30):5458–62.
Article
CAS
PubMed
Google Scholar
Marinaro G, Burghammer M, Costa L, Dane T, De Angelis F, Di Fabrizio E, Riekel C. Directed growth of virus nanofilaments on a superhydrophobic surface. ACS Appl Mater Interfaces. 2015; 7(23):12373–9.
Article
CAS
PubMed
Google Scholar
Chen S-WW, Odorico M, Meillan M, Vellutini L, Teulon JM, Parot P, Bennetau B, Pellequer JL. Nanoscale structural features determined by afm for single virus particles. Nanoscale. 2013; 5:10877–86.
Article
CAS
PubMed
Google Scholar
Trinh MH, Odorico M, Bellanger L, Jacquemond M, Parot P, Pellequer JL. Tobacco mosaic virus as an afm tip calibrator. J Mol Recognit. 2011; 24(3):503–10.
Article
PubMed
Google Scholar
Pernot P, Round A, Barrett R, De Maria Antolinos A, Gobbo A, Gordon E, Huet J, Kieffer J, Lentini M, Mattenet M, Morawe C, Mueller-Dieckmann C, Ohlsson S, Schmid W, Surr J, Theveneau P, Zerrad L, McSweeney S. Upgraded ESRF BM29 beamline for SAXS on macromolecules in solution. J Synchrotron Radiat. 2013; 20(4):660–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Round A, Felisaz F, Fodinger L, Gobbo A, Huet J, Villard C, Blanchet CE, Pernot P, McSweeney S, Roessle M, Svergun DI, Cipriani F. BioSAXS Sample Changer: a robotic sample changer for rapid and reliable high-throughput X-ray solution scattering experiments. Acta Crystallogr D. 2015; 71(1):67–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brennich ME, Kieffer J, Bonamis G, De Maria Antolinos A, Hutin S, Pernot P, Round A. Online data analysis at the ESRF bioSAXS beamline, BM29. J Appl Crystallogr. 2016; 49(1):203–12.
Article
CAS
Google Scholar
De Maria Antolinos A, Pernot P, Brennich ME, Kieffer J, Bowler MW, Delageniere S, Ohlsson S, Malbet Monaco S, Ashton A, Franke D, Svergun D, McSweeney S, Gordon E, Round A. ISPyB for BioSAXS, the gateway to user autonomy in solution scattering experiments. Acta Crystallogr. D. 2015; 71(1):76–85.
Article
PubMed
PubMed Central
Google Scholar
Konarev PV, Volkov VV, Sokolova AV, Koch MH, Svergun DI. Primus: a windows pc-based system for small-angle scattering data analysis. J Appl Crystallogr. 2003; 36(5):1277–82.
Article
CAS
Google Scholar
Svergun DI. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallogr. 1992; 25(4):495–503.
Article
Google Scholar
Spinozzi F, Ferrero C, Ortore MG, De Maria Antolinos A, Mariani P. GENFIT: software for the analysis of small-angle X-ray and neutron scattering data of macromolecules in solution. J Appl Crystallogr. 2014; 47(3):1132–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Svergun D, Barberato C, Koch MHJ. CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates. J Appl Crystallogr. 1995; 28(6):768–73.
Article
CAS
Google Scholar
Hansma PK, Cleveland JP, Radmacher M, Walters DA, Hillner PE, Bezanilla M, Fritz M, Vie D, Hansma HG, Prater CB, Massie J, Fukunaga L, Gurley J, Elings V. Tapping mode atomic force microscopy in liquids. Appl Phys Lett. 1994; 64(13):1738–40.
Article
CAS
Google Scholar
El Kirat K, Burton I, Dupres V, Dufrene YF. Sample preparation procedures for biological atomic force microscopy. J Microsc. 2005; 218(3):199–207.
Article
CAS
PubMed
Google Scholar
Nečas D, Klapetek P. Gwyddion: an open-source software for spm data analysis. Cent Eur J Phys. 2012; 10(1):181–8.
Google Scholar
Chen S-WW, Pellequer JL. Destripe: frequency-based algorithm for removing stripe noises from afm images. BMC Struct Biol. 2011; 11(1):7.
Article
PubMed
PubMed Central
Google Scholar
Lee B, Lo CT, Thiyagarajan P, Winans RE, Li X, Niu Z, Wang Q. Effect of interfacial interaction on the cross-sectional morphology of tobacco mosaic virus using gisaxs. Langmuir. 2007; 23(22):11157–63.
Article
CAS
PubMed
Google Scholar
Kendall A, McDonald M, Stubbs G. Precise determination of the helical repeat of tobacco mosaic virus. Virology. 2007; 369(1):226–7.
Article
CAS
PubMed
Google Scholar
Franklin RE, Klug A. The splitting of layer lines in x-ray fibre diagrams of helical structures: application to tobacco mosaic virus. Acta Crystallogr. 1955; 8(12):777–80.
Article
CAS
Google Scholar
Meillan M, Ramin MA, Buffeteau T, Marsaudon S, Odorico M, Chen S-WW, Pellequer JL, Degueil M, Heuzé K, Vellutini L, et al. Self-assembled monolayer for afm measurements of tobacco mosaic virus (tmv) at the atomic level. RSC Adv. 2014; 4(23):11927–30.
Article
CAS
Google Scholar
Klug A. The tobacco mosaic virus particle: structure and assembly. Philos Trans R Soc Lond B Biol Sci. 1999; 354:531–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Garman EF, Weik M. Radiation damage in macromolecular crystallography. Synchrotron Radiat News. 2015; 28(6):15–9.
Article
Google Scholar
Carpentier P, Royant A, Weik M, Bourgeois D. Raman-assisted crystallography suggests a mechanism of x-ray-induced disulfide radical formation and reparation. Structure. 2010; 18(11):1410–9.
Article
CAS
PubMed
Google Scholar
Bartesaghi A, Matthies D, Banerjee S, Merk A, Subramaniam S. Structure of -galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy. Proc Natl Acad Sci USA. 2014; 111(32):11709–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yoshikawa Y, Hizume K, Oda Y, Takeyasu K, Araki S, Yoshikawa K. Protective effect of vitamin c against double-strand breaks in reconstituted chromatin visualized by single-molecule observation. Biophys J. 2006; 90(3):993–9.
Article
CAS
PubMed
Google Scholar
Jain V, Hassan PA, Das B. Radiation-induced conformational changes in chromatin structure in resting human peripheral blood mononuclear cells. Int J Radiat Biol. 2014; 90(12):1143–51.
Article
CAS
PubMed
Google Scholar
Skou S, Gillilan RE, Ando N. Synchrotron-based small-angle x-ray scattering (saxs) of proteins in solution. Nat Protoc. 2014; 9(7):1727.
Article
CAS
PubMed
PubMed Central
Google Scholar
Philipp HT, Koerner LJ, Hromalik MS, Tate MW, Gruner SM. Femtosecond radiation experiment detector for x-ray free-electron laser (xfel) coherent x-ray imaging. 2008 IEEE Nucl Sci Symp Conf Rec. 2010; 57(6):3795–9.
CAS
Google Scholar
Haas S, Plivelic TS, Dicko C. Combined saxs/uv–vis/raman as a diagnostic and structure resolving tool in materials and life sciences applications. J Phys Chem B. 2014; 118(8):2264–73.
CAS
PubMed
Google Scholar
Lamb J, Kwok L, Qiu X, Andresen K, Park HY, Pollack L. Reconstructing three-dimensional shape envelopes from time-resolved small-angle X-ray scattering data. J Appl Crystallogr. 2008; 41(6):1046–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gumí-Audenis B, Carlà F, Vitorino M, Panzarella A, Porcar L, Boilot M, Guerber S, Bernard P, Rodrigues M, Sanz F, et al. Custom afm for x-ray beamlines: in situ biological investigations under physiological conditions. J Synchrotron Radiat. 2015; 22(6):1364–71.
Article
PubMed
PubMed Central
Google Scholar
Petoukhov MV, Franke D, Shkumatov AV, Tria G, Kikhney AG, Gajda M, Gorba C, Mertens HDT, Konarev PV, Svergun DI. New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr. 2012; 45(2):342–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brennich ME, Kieffer J, Bonamis G, De Maria Antolinos A, Hutin S, Pernot P, Round A. Online data analysis at the ESRF bioSAXS beamline, BM29. J Appl Crystallogr. 2016; 49(1):203–12.
Article
CAS
Google Scholar
Ashiotis G, Deschildre A, Nawaz Z, Wright JP, Karkoulis D, Picca FE, Kieffer J. The fast azimuthal integration Python library: pyFAI. J Appl Crystallogr. 2015; 48(2):510–9.
Article
CAS
PubMed
PubMed Central
Google Scholar