AFM Investigation of the Organization of Actin Bundles Formed by Actin-Binding Proteins

Jamie L. Gilmore, Masahiro Kumeta, Kunio Takeyasu

Graduate School of Biostudies, Kyoto University, Kyoto, Japan..

DOI: 10.4236/jsemat.2013.34A1002                

Abstract

AFM is a powerful technique for revealing the morphological features of various biological systems at high resolution. However, one of the complications of AFM is that samples must be attached to a flat surface in order to obtain images. This often requires the development of specialized methods depending on the sample which is being used. In this study, we developed a novel technique to image actin bundles on the mica surface. Using this technique, we were able to image molecular assemblies of F-actin with two actin remodeling proteins: α-actinin and Caprice. High resolution AFM images of F-actin fibers and bundle organization depicted two different types of molecular assemblies: F-actin bundles forming an elongated “zipper” structure in the presence of α-actinin, and bundles forming a perpendicularly crossing the mesh structure in the presence of Caprice.

Keywords

F-Actin; Caprice; α-Actinin

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	P. Hansma, V. Elings, O. Marti and C. Bracker, “Scanning Tunneling Microscopy and Atomic Force Microscopy: Application to Biology and Technology,” Science, Vol. 242, No. 4876, 1988, pp. 209-216. http://dx.doi.org/10.1126/science.3051380
[2]	G. Binnig, C. Quate and C. Gerber, “Atomic Force Microscope,” Physical Review Letters, Vol. 56, No. 9, 1986, pp. 930-933. http://dx.doi.org/10.1103/PhysRevLett.56.930
[3]	V. Morris, A. Gunning, and A. Kirby, “Atomic Force Microscopy for Biologists,” Imperial College Press, London, 1999. http://dx.doi.org/10.1142/p173
[4]	B. Bhushan, “Scanning Probe Microscopy in Nanoscience and Nanotechnology,” Springer-Verlag Berlin Heidelberg, Berlin, 2010.
[5]	B. Bhushan, “Scanning Probe Microscopy in Nanoscience and Nanotechnology,” Springer-Verlag Berlin Heidelberg, Berlin, 2011.
[6]	K. Takeyasu, “Atomic Force Microscopy in Nano-Biology,” Pan Stanford Publishing Co., Singapore City, 2013.
[7]	Q. Zhong and D. Inniss, “Fractured Polymer/Silica Fiber Surface Studied by Tapping Mode Atomic Force Microscopy,” Surface Science Letters, Vol. 290, No. 1-2, 1993, pp. L688-L692.
[8]	K. Hohmura, Y. Itokazu, S. Yoshimura, G. Mizuguchi, Y. Masamura, K. Takeyasu, et al., “Atomic Force Microscopy with Carbon Nanotube Probe Resolves the Subunit Organization of Protein Complexes,” Journal of Electron Microscopy (Tokyo), Vol. 49, No. 3, 2000, pp. 415-421. http://dx.doi.org/10.1093/oxfordjournals.jmicro.a023823
[9]	J. Gilmore, Y. Suzuki, G. Tamulaitis, V. Siksnys, K. Takeyasu and Y. Lyubchenko, “Single-Molecule Dynamics of the DNA-EcoRII Protein Complexes Revealed with High-Speed Atomic Force Microscopy,” Biochemistry, Vol. 48, No. 44, 2009, pp. 10492-10498. http://dx.doi.org/10.1021/bi9010368
[10]	Y. Suzuki, Y. Higuchi, K. Hizume, M. Yokokawa, S. Yoshimura, K. Yoshikawa, et al., “Molecular Dynamics of DNA and Nucleosomes in Solution Studied by FastScanning Atomic Force Microscopy,” Ultramicroscopy, Vol. 110, No. 6, 2010, pp. 682-688. http://dx.doi.org/10.1016/j.ultramic.2010.02.032
[11]	Y. Suzuki, J. Gilmore, S. Yoshimura, R. Henderson, Y. Lyubchenko and K. Takeyasu, “Visual Analysis of Concerted Cleavage by Type IIF Restriction Enzyme SfiI in Subsecond Time Region,” Biophysical Journal, Vol. 101, No. 12, 2011, pp. 2992-2998. http://dx.doi.org/10.1016/j.bpj.2011.09.064
[12]	H. Sanchez, Y. Suzuki, M. Yokokawa, K. Takeyasu and C. Wyman, “Protein-DNA Interactions in High Speed AFM: Single Molecule Diffusion Analysis of Human RAD54,” Integrative Biology (Camb), Vol. 3, No. 11, 2011, pp. 1127-1134. http://dx.doi.org/10.1039/c1ib00039j
[13]	M. Yokokawa, C. Wada, T. Ando, N. Sakai, A. Yagi, S. Yoshimura, et al., “Fast-Scanning Atomic Force Microscopy Reveals the ATP/ADP-Dependent Conformational Changes of GroEL,” The EMBO Journal, Vol. 25, No. 19, 2006, pp. 4567-4576. http://dx.doi.org/10.1038/sj.emboj.7601326
[14]	N. Kodera, D. Yamamoto, R. Ishikawa and T. Ando, “Video Imaging of Walking Myosin V by High-Speed Atomic Force Microscopy,” Nature, Vol. 468, No. 7320, 2010, pp. 72-76. http://dx.doi.org/10.1038/nature09450
[15]	M. Yokokawa and K. Takeyasu, “Motion of the Ca2+ Pump Captured,” FEBS Journal, Vol. 278, No. 17, 2011, pp. 3025-3031. http://dx.doi.org/10.1111/j.1742-4658.2011.08222.x
[16]	M. Shibata, T. Uchihashi, H. Yamashita, H. Kandori and T. Ando, “Structural Changes in Bacteriorhodopsin in Response to Alternate Illumination Observed by HighSpeed Atomic Force Microscopy,” Angewandte Chemie International Edition, Vol. 50, No. 19, 2011, pp. 4410-4413. http://dx.doi.org/10.1002/anie.201007544
[17]	Y. Suzuki, T. Goetze, D. Stroebel, D. Balasuriya, S. Yoshimura, R. Henderson, et al., “Visualization of Structural Changes Accompanying Activation of N-Methyl-D-Aspartate (NMDA) Receptors Using Fast-Scan Atomic Force Microscopy Imaging,” The Journal of Biological Chemistry, Vol. 288, No. 2, 2013, pp. 778-784. http://dx.doi.org/10.1074/jbc.M112.422311
[18]	N. Crampton, M. Yokokawa, D. Dryden, J. Edwardson, D. Rao, K. Takeyasu, et al., “Fast-Scan Atomic Force Microscopy Reveals That the Type III Restriction Enzyme EcoP15I is Capable of DNA Translocation and Looping,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 31, 2007, pp. 12755-12760. http://dx.doi.org/10.1073/pnas.0700483104
[19]	Y. Hirano, K. Ishii, M. Kumeta, K. Furukawa, K. Takeyasu and T. Horigome, “Proteomic and Targeted Analytical Identification of BXDC1 and EBNA1BP2 as Dynamic Scaffold Proteins in the Nucleolus,” Genes Cells, Vol. 14, No. 2, 2009, pp. 155-166. http://dx.doi.org/10.1111/j.1365-2443.2008.01262.x
[20]	M. Kumeta, Y. Hirai, S. Yoshimura, T. Horigome and K. Takeyasu, “Antibody-Based Analysis Reveals ‘Filamentous vs. Non-Filamentous’ and ‘Cytoplasmic vs. Nuclear’ Crosstalk of Cytoskeletal Proteins,” Experimental Cell Research, in Press.
[21]	M. Zhu, F. Settele, S. Kotak, L. Sanchez-Pulido, L. Ehret, C. Ponting, et al., “MISP Is a Novel Plk1 Substrate Required for Proper Spindle Orientation and Mitotic Progression,” The Journal of Cell Biology, Vol. 200, No. 6, 2013, pp. 773-787. http://dx.doi.org/10.1083/jcb.201207050
[22]	K. Zechel and K. Weber, “Actins from Mammals, Bird, Fish and Slime Mold Characterized by Isoelectric Focusing in Polyacrylamide Gels,” European Journal of Biochemistry, Vol. 89, No. 1, 1978, pp. 105-112. http://dx.doi.org/10.1111/j.1432-1033.1978.tb20901.x
[23]	S. Sharma, E. Grintsevich, M. Phillips, E. Reisler and J. Gimzewski, “Atomic Force Microscopy Reveals Drebrin Induced Remodeling of F-Actin with Subnanometer Resolution,” Nano Letters, Vol. 11, No. 2, 2011, pp. 825-827. http://dx.doi.org/ 10.1021/nl104159v
[24]	T. Ikawa, F. Hoshino, O. Watanabe, Y. Li, P. Pincus and C. Safinya, “Molecular Scale Imaging of F-Actin Assemblies Immobilized on a Photopolymer Surface,” Physical Review Letters, Vol. 98, No. 1, 2007, Article ID: 01801. http://dx.doi.org/10.1103/PhysRevLett.98.018101
[25]	Z. Shao, D. Shi and A. Somlyo, “Cryoatomic Force Microscopy of Filamentous Actin,” Biophysical Journal, Vol. 78, No. 2, 2000, pp. 950-958. http://dx.doi.org/10.1016/S0006-3495(00)76652-5
[26]	D. Shi, A. Somlyo, A. Somlyo and Z. Shao, “Visualizing Filamentous Actin on Lipid Bilayers by Atomic Force Microscopy in Solution,” Journal of Microscopy, Vol. 201, No. Pt 3, 2001, pp. 377-382.
[27]	R. Meyer and U. Aebi, “Bundling of Actin Filaments by Alpha-Actinin Depends on its Molecular Length,” The Journal of Cell Biology, Vol. 110, No. 6, 1990, pp. 2013-2024. http://dx.doi.org/10.1083/jcb.110.6.2013
[28]	S. Ebashi and F. Ebashi, “A New Protein Promoting Contraction of Actomyosin,” Nature, Vol. 203, No. 4945, 1964, pp. 645-646. http://dx.doi.org/10.1038/203645a0
[29]	D. Goli, A. Suzuki, J. Temple and G. Holmes, “Studies on Purified-Actinin. I. Effect of Temperature and Tropomyosin on the Actinin-F-Actin Interaction,” Journal of Molecular Biology, Vol. 67, No. 3, 1972, pp. 469-488.
[30]	O. Pelletier, E. Pokidysheva, L. Hirst, N. Bouxsein, Y. Li and C. Safinya, “Structure of Actin Cross-Linked with Alpha-Actinin: A Network of Bundles,” Physical Review Letters, Vol. 91, No. 14, 2003, Article ID: 148102. http://dx.doi.org/10.1103/PhysRevLett.91.148102
[31]	B. Knight, C. Laukaitis, N. Akhtar, N. Hotchin, M. Edlund and A. Horwitz, “Visualizing Muscle Cell Migration in Situ,” Current Biology, Vol. 10, No. 10, 2000, pp. 576-585. http://dx.doi.org/10.1016/S0960-9822(00)00486-3
[32]	J. Ylanne, K. Scheffzek, P. Young and M. Saraste, “Crystal Structure of the Alpha-Actinin Rod Reveals an Extensive Torsional Twist,” Structure, Vol. 9, No. 7, 2001, pp. 597-604. http://dx.doi.org/10.1016/S0969-2126(01)00619-0
[33]	B. Sjoblom, A. Salmazo and K. Djinovic-Carugo, “Alpha-Actinin Structure and Regulation,” Cellular and Molecular Life Sciences, Vol. 65, No. 17, 2008, pp. 2688-2701. http://dx.doi.org/10.1007/s00018-008-8080-8
[34]	K. Ishii, Y. Hirano, N. Araki, T. Oda, M. Kumeta, K. Takeyasu, et al., “Nuclear Matrix Contains Novel WDRepeat and Disordered-Region-Rich Proteins,” FEBS Letters, Vol. 582, No. 23-24, 2008, pp. 3515-3519.