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Bruce Baumann

Bruce “Sandy” Baumann

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Jinghua Tang

  • Assistant Project Scientist (under Prof. Timothy Baker)
  • Dept. Chemistry and Biochemistry, UCSD
  • 4107 Natural Sciences Bldg., MC-0378
  • La Jolla, CA 92093

I was a PhD student in dr. Taylor’s lab from 1995-2000. For my dissertation, I obtained a 3-D reconstructed image of skeletal muscle α-ctinin and built a pseudo atomic model.

α-Actinin is an F-actin binding and cross-linking protein. It is an antiparallel homodimer, with a subunit molecular weight of 94-103 KD. It is visualized as a long rod-shaped molecule in the electron microscope, 3-4 nm wide and 30-40 nm in length. Alpha-actinin is a structural protein, so its physiological importance lies in what it interacts with and where. The F-actin cross-linking activity is its best known physiological role. It also mediates linkages between plasma membrane and cytoskeleton. Alpha-actinin is found in a wide variety of cells. The best known subcellular location is the Z-disk of striated muscle where it crosslinks antiparallel actin filaments to form the I-band. In smooth muscle, alpha-actinin is found in both cytoplasmic dense bodies and membrane associated adhesion plaques. In non-muscle cells, alpha-actinin appears in stress fibers and focal adhesions. It has been shown to associate with spectrin, nebulin and tropomyosin, ICAM-1, L-selectin and beta1- and beta2-integrins and talin, vinculin, and zyxin. Alpha-actinin is also linked to the phospholipid signal pathways by its interactions with phosphatidylinositol 4,5-biphosphate and phosphoinositide 3-kinase.

Recent Publications

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Thomas Wendt

  • Leiter Pägogik & Labore experimenta – Science Center der Region Heilbronn-Franken gGmbH
  • Geschässtelle: Kramstr. 1, 74072 Heilbronn
  • Tel. +49 (0)7131 97 339-32   Fax +49 (0)7131 56-2859
  • Personal web page
  • thomas.wendt@experimenta-heilbronn.de

 

I was a postdoctoral scientist in Prof. Taylor’s laboratory from 1998 to 2001. My project was to determine the structure of the inhibited conformation of smooth muscle HMM and myosin. I used electron crystallography of 2-D arrays of dephosphorylated smooth muscle HMM. The protein was expressed by Dr. Kathy Trybus and the crystallography was done using frozen hydrated specimens. This is a unique capability of Prof. Taylor’s laboratory. The 3-D reconstructions showed an unusual interaction between the two myosin heads that explained most of the biochemistry of the inhibited state of this myosin. The result obtained with the HMM fragment was later confirmed using full length smooth muscle myosin and later by work done in the laboratory of Dr. Roger Craig in tarantula myosin filaments.

 


Figure Legend: Averaged projection of smooth muscle heavy meromyosin in the dephosphorolated state preserved frozen hydrated in amorphous ice. 2D array was grown on a lipid monolayer. Smooth muscle heavy meromyosin (HMM) is a truncated double-headed myosin molecule. Two-dimensional crystals bound to a lipid monolayer were examined by cryo-electron microscopy on a 300keV FEG microscope. Data was collected for untilted and tilted specimen and a 2D projection map was calculated giving a resolution of 2.8 nm. The crystals show unit cell dimensions of 12.9 by 28.1 nm suggesting that there are 2 HMM molecules per unit cell with P2 symmetry.

Publications

  • Thomas Wendt, Dianne Taylor, Kathy Trybus, Terri Messier and Kenneth A. Taylor. Visualization of head-head interactions in the inhibited state of smooth muscle myosin. J. Cell Biol. 147, 1385-1390 (1999)
  • Thomas Wendt, Dianne Taylor, Kathleen M. Trybus, and Kenneth Taylor. 3-D image reconstruction of dephosphorylated smooth muscle heavy meromyosin reveals asymmetry in the interaction between myosin heads and placement of subfragment 2. Proc. Natl. Acad. Sci. 98(8), 4361-4366 (2001)
  • Jun Liu, Thomas Wendt, Dianne W. Taylor and Kenneth A. Taylor. Refined model of the 10S conformation of smooth muscle myosin by cryoEM 3-D image reconstruction. J. Mol. Biol. 329(5), 963-972 (2003)
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Lifan Chen


 

  • Research Scientist
  • Senior Principal Engineer
  • Western Digital Corporation
  • 44100 Osgood Rd.
  • Fremont, CA 94539
  • lfchen02@yahoo.com

I was a post doc in Professor Taylor’s lab from 1997-1999. I came from a material science background. This was my first appointment into a structural biology laboratory. My work involved building and reforming atom models into 3-D volumes obtained by electron tomography of insect flight muscle in rigor.

Lattice constraints as well as differences in biochemical state of the independently acting myosin heads result in structural variations in situ that depart significantly from the uniform structure that is obtained by X-ray crystal structures. Our aim is to fit initially the atomic model for rigor acto-S1 complex into the envelope of 3-D reconstructions obtained by electron tomography. Adjustments are then made to the atomic model manually using the crystallography program “O” to correct for regions where model and envelope differ. Adjustments in the atomic model at this point are restricted to the light chain domain, which is pivoted about residue 770 of the myosin heavy chain. The motor domain and the actin monomers are kept constant. We have developed a procedure for correcting poor contacts that are produced by these manual adjustments using the RSref program. RSref is a real space refinement program that compares the electron density of the model with the density map. Movements of the model are determined using conjugate gradients. An independent scale factor is used to account for overall differences in density between model and map. The TNT refinement program is used in parallel to determine the corrections needed to improve poor geometry. A set of initial constraints is used to limit movements of the model. One of these involves maintaining the C-terminal residues of the two heavy chains to a minimum separation. Results obtained by modeling the acto-S1 structure into the envelope of the 2-headed crossbridge in rigor insect flight muscle show a range of axial movement in the light chain domain comparable to those hypothesized for muscle contraction. In addition, azimuthal movements are required to bring the two heavy chains into proximity.

Figure Legend. This picture shows an atomic model of an opposed pair of 2-headed myosin crossbridges attached to an actin filament. The model has been fit to an electron density map of insect flight muscle in the rigor state. The 3-D map was obtained by electron tomography of a section of plastic embedded tissue. The model was developed starting with the coordinates of rigor acto-S1 developed by Ivan Rayment and coworkers. We then moved the C-terminal residues to within 12Å of each other by pivoting the light chain domains of both S1s about residue 770. Then RSref was run to correct poor geometry and iverlaping domains. The rsulting model fits the electron density much better than the original starting model which had considerable density falling outside of the 3-D envelope. This project done in collaboration with the laboratories of Michael Chapman at Florida State University and Michael and Mary Reedy at Duke University.

 

PUBLICATIONS

  • L.F. Chen, M. S. Chapman, E. Blanc and K. A. Taylor. Modeling the atomic structure of myosin S1 and actin into 3-D reconstructions of insect flight muscle. Biophys. J. 74, A22 (1998)
  • Kenneth A. Taylor, Holger Schmitz, Mary C. Reedy, Yale E. Goldman, Clara Franzini-Armstrong, Hiro Sasaki, Richard T. Tregear, Kate Poole, Carmen Lucaveche, Robert J. Edwards, Li Fan Chen, Hanspeter Winkler, and Michael K. Reedy. Tomographic 3-D reconstruction of quick frozen, Ca++-activated contracting insect flight muscle. Cell 99, 421-431 (1999).
  • Li Fan Chen, Eric Blanc, Michael S. Chapman and Kenneth A. Taylor. Real space refinement of acto-myosin structures from sectioned muscle. J. Struct. Biol. 133(2), 221-232 (2001)
  • Chen, Li Fan, Winkler, Hanspeter, Reedy, Michael K., Reedy, Mary C. & Taylor ,Kenneth A.. Molecular Modeling of Averaged Rigor Crossbridges from Tomograms of Insect Flight Muscle. J. Struct. Biol., 138(2), 92-104 (2002)
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Yifan Cheng

  • Dept. of Biochemistry & Biophysics
  • University of California San Francisco
  • Genentech Hall Room S312B
  • 600 16th Street
  • San Francisco, CA 94158-2517
  • Telephone: (415) 514-9707
  • FAX: (415) 514-4145
  • ycheng@biochem.ucsf.edu

 


I was a postdoc in Professor Taylor’s lab from 1996-1998. I came from a material science background and this was my first appointment in a structural biology laboratory.

My work involved applying the techniques of electron tomography and electron crystallography to the study of protein structure. The laboratory studies mainly muscle proteins, one of which is the actin crosslinking protein alpha-actinin. To facilitate our structural studies, we purchased a Philips CM300-FEG electron microscope and one of my jobs was to evaluate its suitability for electron tomography and protein crystallography. These methods require that the microscope perform well at low magnification. Tests of our microscope showed that 2.04Å lattice fringes from crystalline gold can be obtained at magnifications as low as 10,000X. I have also developed a computer program to record a complete tilt series of any set of angles on the CM300 and CM120 microscopes. This program was used at Florida State University for several years to record tilt series of ice embedded specimens as well as plastic sections on film. They now use a CCD camera to record the tomographic data.


PUBLICATIONS

  • Kenneth A. Taylor, Jinghua Tang, Yifan Cheng, Hanspeter Winkler. The use of electron tomography for structural analysis of disordered protein arrays. J. Struct. Biol. 120, 372-386 (1997)
  • Yifan Cheng, Kenneth A. Taylor. Characterization of the low magnification performance of a Philips CM300-FEG. Ultramicroscopy 74, 209-220 (1998).
  • Jun Liu, Shenping Wu, Mary C. Reedy, Hanspeter Winkler, Carmen Lucaveche, Yifan Cheng, Michael K. Reedy, and Kenneth A. Taylor. Electron tomography of swollen rigor fibers of insect flight muscle reveals a short and variably angled S2 domain. J. Mol. Biol. 362, 844-860 (2006).
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Cindy Le


 

  • University of Florida
  • College of Medicine

 


Insect flight muscle (IFM) is one of the most highly ordered muscles in nature. This high degree of order makes it an ideal specimen for studying different crossbridge states in muscle contraction and for investigating steric constraints that affect the binding of crossbridges to actin. IFM is unique among striated muscles in that not all myosin heads can attach to actin in the rigor state. Thus, the rigor state of IFM contains both 1-headed and 2-headed crossbridges. A explanation for this phenomenon has not been found. The single-headed crossbridges bind actin near the location of the troponin complex. Thus, one possibility is that the troponin complex in IFM blocks binding of the second myosin head. If so, troponin may block the binding of exogenous S1. Previous results suggested that as many as one actin out of seven could be free of S1 (Goody et al., Biophys. J. 47, 151-169 (1985)). To test this possibility we are using electron tomography combined with 3-D correspondence analysis. Troponin is readily identified in EMs and 3-D reconstructions of IFM. Specimens consist of rigor IFM which had been soaked in chymotryptic S1 and were the same specimens in the earlier study. Tomograms were computed using cross correlation methods to align the images and Whittaker-Shannon interpolation of the 3-D transform data. Each 38.7 nm thin filament repeat was extracted from the 3-D reconstruction and subjected to 3-D alignment and correspondence analysis. Hierarchical ascendant classification combined with multireference alignment was used to produce 10 class averages. Each class average shows significant density added along the entire thin filament but particularly shows density at the troponin location. Since the resolution is sufficient to resolve myosin heads, we conclude that troponin does not block S1 binding. It seems therefore likely that lattice constraints prevent the second myosin head of 1-headed crossbridges from binding to actin.

Figure shows an electron micrograph and computed transform of ifm soaked in myosin s1 which reveal high intensity along 5.9 nm 5.1 layer lines from f-actin. This observation indicates good preservation of the actin structure. Magnification insert on left arrowhead structure expected thin filaments.

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