Abstract
Visualization of macromolecular structures is essential for understanding the mechanisms of biological functions because they are all determined by the structure and dynamics of macromolecular complexes. Electron cryomicroscopy (cryoEM) and image analysis has become a powerful tool for structural studies because of recent technical developments in microscope optics, cryostage control, image detection and the methods of sample preparation. In particular, the recent development of CMOS-based direct electron detectors with high sensitivity, high resolution and high frame rate has revolutionized the field of structural biology by making near-atomic resolution structural analysis possible from small amounts of solution samples. However, for some biological systems, it is still difficult to reach high resolution due to somewhat flexible nature of the structure, and a complementary use of cryoEM with X-ray crystallography is essential and useful to gain mechanistic understanding of the biological functions and mechanisms. We will describe our strategy for the structural analyses of actin filament and actomyosin rigor complex and the biological insights we gained from these structures.
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References
Banerjee C, Hu Z, Huang Z, Warrington JA, Taylor DW, Trybus KM, Lowey S, Taylor KA (2017) The structure of the actin-smooth muscle myosin motor domain complex in the rigor state. J Struct Biol 200:325–333
Bauer CB, Holden HM, Thoden JB, Smith R, Rayment I (2000) X-ray Structures of the Apo and MgATP-bound States of Dictyostelium discoideum Myosin Motor Domain. J Biol Chem 275:38494–38499
Behrmann E, Müller M, Penczek PA, Manherz HG, Manstein D, Raunser S (2012) Structure of the rigor actin-tropomyosin-myosin complex. Cell 150:327–338
Cao E, Liao M, Cheng Y, Julius D (2013) TRPV1 structures in distinct conformations reveal activation mechanisms. Nature 504:113–118
Carlier MF, Pantaloni D (2007) Control of actin assembly dynamics in cell motility. J Biol Chem 282:23005–23009
Coureux PD, Wells AL, Ménétry J, Yengo CM, Morris CA, Sweeney HL, Houdusse A (2003) A structural state of the myosin V motor without bound nucleotide. Nature 425:419–423
Dominguez R, Freyzon Y, Trybus KM, Cohen C (1998) Crystal structure of a vertebrate smooth muscle myosin motor domain and its complex with the essential light chain: visualization of the pre-power stroke state. Cell 94:559–571
Egelman EH (2000) A robust algorithm for the reconstruction of helical filaments using single-particle methods. Ultramicroscopy 85:453–463
Fujii T, Namba K (2017) Structure of actomyosin rigour complex at 5.2 Å resolution and insights into the ATPase cycle mechanism. Nature Commun 8:13969 (11pp)
Fujii T, Kato T, Namba K (2009) Specific arrangement of α-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function. Structure 17:1485–1493
Fujii T, Iwane AH, Yanagida T, Namba K (2010) Direct visualization of secondary structures of F-actin by electron cryomicroscopy. Nature 467:724–728
Fujiwara I, Vavylonis D, Pollard TD (2007) Polymerization kinetics of ADP- and ADP-Pi-actin determined by fluorescence microscopy. Proc Natl Acad Sci U S A 104:8827–8832
Fujiyoshi Y, Mizusaki T, Morikawa K, Yamagishi H, Aoki Y, Kihara H, Harada Y (1991) Development of a superfluid helium stage for high-resolution electron microscopy. Ultramicroscopy 38:241–251
Galkin VE, Orlova A, Cherepanova O, Lebart MC, Egelman EH (2008) High-resolution cryo-EM structure of the F-actin-fimbrin/plastin ABD2 complex. Proc Natl Acad Sci U S A 105:1494–1498
Gayathri P, Fujii T, Møller-Jensen J, van den Ent F, Namba K, Löwe J (2012) A bipolar spindle of antiparallel ParM filaments drives bacterial plasmid segregation. Science 338:1334–1337
Geeves MA, Goody RS, Gutfround H (1984) Kinetics of acto-S1 interaction as a guide to a model of the crossbridge cycle. J Muscle Res Cell Motil 5:351–356
Holmes KC, Angert I, Kull FJ, Jahn W, Schröder RR (2003) Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide. Nature 425:423–427
Holmes KC, Schroder RR, Sweeney HL, Houdusse A (2004) The structure of the rigor complex and its implications for the power stroke. Philos Trans R Soc B 359:1819–1828
Houdusse A, Szent-Gyögyi AG, Cohen C (2000) Three conformatinoal states of scallop myosin S1. Proc Natl Acad Sci U S A 97:11238–11243
Huxley HE (1969) The mechanism of muscular contraction. Science 164:1356–1365
Iwaki M, Iwane AH, Shimokawa T, Cooke R, Yanagida T (2009) Brownian search-and-catch mechanism for myosin-VI steps. Nature Chem Biol 5:403–405
Kabsch W, Mannherz HG, Suck D, Pai EF, Holmes KC (1990) Atomic model of the actin:DNase I complex. Nature 347:37–44
Kimanius D, Forsberg BO, Scheres SH, Lindahl E (2016) Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. elife 15:e18722
Kimura Y, Vassylyev DG, Miyazawa A, Kidera A, Matsushima M, Mitsuoka K, Murata K, Hirai T, Fujiyoshi Y (1997) Surface of bacteriorhodopsin revealed by high-resolution electron crystallography. Nature 389:206–211
Kitamura K, Tokunaga M, Iwane AH, Yanagida T (1999) A single myosin head moves along an actin filament with regular steps of 5.3 nanometres. Nature 397:129–134
Li X, Mooney P, Zheng S, Booth CR, Braunfeld MB, Gubbens S, Agard DA, Cheng Y (2013) Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods 10:584–590
Liao M, Cao E, Julius D, Cheng Y (2013) Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504:107–112
Llinas P, Isabet T, Song L, Ropars V, Zong B, Benisty H, Sirigu S, Morris C, Kikuti C, Safer D, Sweeney HL, Houdusse A (2015) How actin initiates the motor activity of myosin. Develop Cell 33:401–412
Lymn RW, Taylor EW (1971) Mechanism of adenosine triphosphate hydrolysis by actomyosin. Biochemist 10:4617–4624
Ménétry J, Bahloul A, Wells AL, Yengo CM, Morris CA, Sweeney HL, Houdusse A (2005) The structure of the myosin VI motor reveals the mechanism of directionality reversal. Nature 435:779–785
Ménétry J, Llinas P, Cicolari J, Squires G, Liu X, Li A, Sweeney HL, Houdusse A (2008) The post-rigor structure of the myosin VI and implications for the recovery stroke. EMBO J 27:244–252
Mentes A, Huehn A, Liu X, Zwolak A, Dominguez R, Shuman H, Ostap EM, Sindelar CV (2018) High-resolution cryo-EM structures of actin-bound myosin states reveal the mechanism of myosin force sensing. Proc Natl Acad Sci U S A 115:1292–1297
Mimori Y, Yamashita I, Murata K, Fujiyoshi Y, Yonekura K, Toyoshima C, Namba K (1995) The structure of the R-type straight flagellar filament of Salmonella at 9 Å resolution by electron cryomicroscopy. J Mol Biol 249:69–87
Mitsuoka K, Hirai T, Murata K, Miyazawa A, Kidera A, Kimura Y, Fujiyoshi Y (1999) The structure of bacteriorhodopsin at 3.0 A resolution based on electron crystallography: implication of the charge distribution. J Mol Biol 286:861–882
Miyazawa A, Fujiyoshi Y, Unwin N (2003) Structure and gating mechanism of the acetylcholine receptor pore. Nature 423:949–955
Murata K, Mitsuoka K, Hirai T, Walz T, Agre P, Heymann JB, Engel A, Fujiyoshi Y (2000) Structural determinants of water permeation through aquaporin-1. Nature 407:599–605
Nagy B, Jencks WP (1965) Depolymerization of F-actin by concentrated solutions of salts and denaturing agents. J Am Chem Soc 87:2480–2488
Namba K, Stubbs G (1985) Solving the phase problem in fiber diffraction. Application to tobacco mosaic virus at 3.6A resolution. Acta Crystallogr A41:252–262
Namba K, Stubbs G. (1986) Structure of tobacco mosaic virus at 3.6 Å resolution: implications for assembly. Science 231:1401–1406
Oda T, Iwasa M, Aihara T, Maeda Y, Narita A (2009) The nature of the globular- to fibrous-actin transition. Nature 457:441–445
Otterbein LR, Graceffa P, Dominguez R (2001) The crystal structure of uncomplexed actin in the ADP state. Science 293:708–711
Pollard TD, Borisy GG (2003) Cellular motility driven by assembly and disassembly of actin filaments. Cell 112:453–465
Rayment, I., Rypniewski,W. R., Schmidt-Bäse, K., Smith, R., Tomchick, D. R., Benning, M. M., Winkelmann D. A., Wesenberg, G. & Holden HM. (1993) Three-dimensional structure of myosin subfragment-1: a molecular motor. Science 261, 50–58
Reubold TF, Eschenburg S, Becker A, Kull FJ, Manstein DJ (2003) A structural model for actin-induced nucleotide release in myosin. Nature Struct Biol 10:826–830
Reubold, T. F., Eschenburg, S., Becker, Loonard, M, Schmid, S. L., Vallee, R. B., Kull, F. J. & Manstein, D. J. (2005) Crystal structure of the GTPase domain of rat dynamin 1. Proc Natl Acad Sci U S A 102, 13093–13098
Sachse C, Chen JZ, Coureux P, Stroupe ME, Fandrich M, Grigorieff N (2007) High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus. J Mol Biol 371:812–835
Samatey FA, Imada K, Nagashima S, Kumasaka T, Yamamoto M, Vonderviszt F, Namba K (2001) Structure of the bacterial flagellar protofilament and implication for a switch for supercoiling. Nature 410:331–337
Samatey FA, Matsunami H, Imada K, Nagashima S, Shaikh TR, Thomas DR, Chen JZ, Derosier DJ, Namba K (2004) Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism. Nature 431:1062–1068
Scheres SH (2012) RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 180:519–530
Schroder GF, Brunger AT, Levitt M (2007) Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Struct 15:1630–1641
Sweeney HL, Houdusse A (2004) The motor mechanism of myosin V: insights for muscle contraction. Philos Trans R Soc B 359:1829–1841
Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A (2008) Protein structure fitting and refinement guided by cryo-EM density. Struct. 16:295–307
von der Ecken J, Heissler SM, Pathan-Chhatbar S, Manstein DJ, Raunser S (2016) Cryo-EM structure of a hyman cytoplasmic actomyosin complex at near-atomic resolution. Nature 354:724–728
Wulf SF, Roparsb V, Fujita-Beckera S, Ostera M, Hofhausa G, Trabucoc LG, Pylypenkob O, Sweeney HL, Houdusseb AM, Schröder R (2016) Force-producing ADP state of myosin bound to actin. Proc Natl Acad Sci U S A 113:E1844–E1852
Yanagida T, Arata T, Oosawa F (1985) Sliding distance of actin filament induced by a myosin crossbridge during one ATP hydrolysis cycle. Nature 316:366–369
Yang Y, Gourinath S, Kovács M, Mitray L, Reutzel R, Himmel DM, O'Neall-Hennessey E, Reshetnikova L, Szent-Györgyi AG, Brown JH, Cohen C (2007) Rigor-like structures from muscle myosins reveal key mechanical elements in the transduction pathways of this allosteric motor. Structure 15:553–564
Yonekura K, Maki-Yonekura S, Namba K (2003) Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature 424:643–650
Yount RG, Lawson D, Rayment I (1995) Is myosin a “Back Door” Enzyme? Biophys J 68:44s–49s
Acknowledgement
This work was supported by JSPS KAKENHI Grant number 25711010 to T.F and 25000013 to K.N.
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Fujii, T., Namba, K. (2018). Complementary Use of Electron Cryomicroscopy and X-Ray Crystallography: Structural Studies of Actin and Actomyosin Filaments. In: Nakamura, H., Kleywegt, G., Burley, S., Markley, J. (eds) Integrative Structural Biology with Hybrid Methods. Advances in Experimental Medicine and Biology, vol 1105. Springer, Singapore. https://doi.org/10.1007/978-981-13-2200-6_4
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