Steven J. Ludtke

Associate Professor of Biochemistry and Molecular Biology and Co-director of the National Center for Macromolecular Imaging  at Baylor College of Medicine (not affiliated with Baylor University) Grad. School: Rice University, PhD in Physics 1996 Undergrad: Caltech (Lloyd House), graduated 1990 Check my curriculum vitae for more. I also have a personal home page.

My work involves the 3D reconstruction of molecules and macromolecules using a technique called single particle reconstruction. My most significant contribution to the field is the development of the EMAN software suite, which performs semi-automated processing of electron cryomicrographs to produce accurate 3D reconstructions at subnanometer resolutions. In this technique, a solution containing large molecules and macromolecular assemblies is vitrified (frozen in non-crystalline ice) on an electron microscope grid. It is then imaged at liquid helium or liquid nitrogen temperatures on a transmission electron microscope. Images of individual molecules/assemblies are then collected. These images are very noisy, but represent the solution-like structure of the molecule under study. A large number (1000-100,000) of these particles are then processed using a series of algorithms (implemented in EMAN) to produce accurate volumetric reconstructions of the molecule at resolutions now approaching 0.5 nm (slightly worse than atomic resolution). This technique can also be applied to heterogeneous specimens, such as those existing in multiple functional states.

A growing number of labs around the world are now equipped to collect data using this technique. The NCMI, as an NCRR funded center, participates in both collaborative and service projects using its 4 state of the art electron cryomicroscopes. Visit the NCMI home page if you are interested in performing an experiment using our facilities.

Publications:

CryoEM Related

• Hohn, M., Tang, G., Goodyear, G., Baldwin, P.R., Huang, Z., Penczek, P.A., Yang, C., Glaeser, R.M, Adams, P.D., and Ludtke, S.J. (2007). SPARX, a new environment for Cryo-EM image processing. J Struct Biol. 157:47-55.
• Tang, G., Peng, L., Baldwin, P. R., Mann, D. S., Jiang, W., Rees, I., and Ludtke, S. J. (2007). EMAN2: An extensible image processing suite for electron microscopy. J Struct Biol. 157:38-46.
• Chen, D.H., Song, J.L., Chuang, D.T., Chiu, W., Ludtke, S.J. (2006). An expanded conformation of single-ring GroEL-GroES complex encapsulates an 86 kDa substrate. Structure. 11:1711-1722.
• Jiang, X., Jayaram, H., Kumar, M., Ludtke, S. J., Estes, M. K., and Prasad, B. V. (2006). Cryo-EM Structures of Rotavirus NSP2-NSP5 and NSP2-RNA Complexes: Implications for Genome Replication. J Virol. 80:10829-35.
• Arac, D., Chen, X., Khant, H.A., Ubach, J., Ludtke, S.J., Kikkawa, M., Johnson, A.E., Chiu, W., Sudhof, T.C., Rizo, J. (2006) Close membrane-membrane proximity induced by Ca(2+)-dependent multivalent binding of synaptotagmin-1 to phospholipids. Nat Struct Mol Biol. 13(3):209-17.
• Passmore, L.A., Booth, C.R., Venien-Bryan, C., Ludtke, S.J., Fioretto, C., Johnson, L.N., Chiu, W., Barford, D. (2005) Structural analysis of the anaphase-promoting complex reveals multiple active sites and insights into polyubiquitylation. Mol Cell. 20(6):855-66.
• Yu, X., Acehan, D., Menetret, J.F., Booth, C.R., Ludtke, S.J., Riedl, S.J., Shi, Y., Wang, X. and Akey, C.W.. (2005) A structure of the human apoptosome at 12.8 Å resolution provides insights into this cell death platform. Structure. 13:1725-35.
• Jiang W, Ludtke SJ. (2005) Electron cryomicroscopy of single particles at subnanometer resolution. Curr Opin Struct Biol. 15(5):571-7
• Ludtke, S.J., Serysheva, I.I., Hamilton, S.L. and Chiu, W. (2005) The pore structure of the closed RyR1 channel. Structure. 8:1203-11.
• Sitharaman, B., Kissell, K.R., Hartman, K.B., Tran, L.A., Baikalov, A., Rusakova, I., Sun, Y., Khant, H.A., Ludtke, S.J., Chiu, W., Laus, S., Toth, E., Helm, L., Merbach, A.E. and Wilson, L.J.. (2005) Superparamagnetic gadonanotubes are high-performance MRI contrast agents. Chem. Commun. 31:3915-7.
• Menetret, J.F., Hegde, R.S., Heinrich, S.U., Chandramouli, P., Ludtke, S.J., Rapoport, T.A., and Akey, C.W. (2005). Architecture of the ribosome-channel complex derived from native membranes. J. Mol. Biol. 348,445-57.
• Serysheva, I.I, Hamilton, S.L., Chiu, W., Ludtke, S.J. (2005). Structure of Ca²⁺ Release Channel at 14 Å Resolution. J. Mol. Biol., 345, 427-431.
• Zhu, Y., Carragher, B., Glaeser, R.M., Fellmann, D., Bajaj, C., Bern, M., Mouche, F., de Haas, F., Hall, R.J., Kriegman, D.J., Ludtke, S.J., Mallick, S.P., Penczek, P.A., Roseman, A.M., Sigworth, F.J., Volkmann, N., and Potter, C.S. (2004). Automatic particle selection: results of a comparative study. J Struct Biol 145, 3-14.
• Mao, Y., Vyas, N.K., Vyas, M.N., Chen, D.H., Ludtke, S.J., Chiu, W., and Quiocho, F.A. (2004). Structure of the bifunctional and Golgi-associated formiminotransferase cyclodeaminase octamer. Embo J 23, 2963-2971.
• Ludtke, S.J., Chen, D.H., Song, J.L., Chuang, D.T., and Chiu, W. (2004). Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy. Structure (Camb) 12, 1129-1136.
• Chen, C., Ko, Y., Delannoy, M., Ludtke, S.J., Chiu, W., and , P.L. Pedersen (2004). Mitochondrial ATP synthasome: three-dimensional structure by electron microscopy of the ATP synthase in complex formation with carriers for Pi and ADP/ATP. J Biol Chem 279, 31761-31768.
• Brink, J., Ludtke, S.J., Kong, Y., Wakil, S.J., Ma, J., and Chiu, W. (2004). Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis. Structure (Camb) 12, 185-191.
• Booth, C.R., Jiang, W., Baker, M.L., Zhou, Z.H., Ludtke, S.J., and Chiu, W. (2004). A 9 angstroms single particle reconstruction from CCD captured images on a 200 kV electron cryomicroscope. J Struct Biol 147, 116-127.
• Serysheva, II, Bare, D.J., Ludtke, S.J., Kettlun, C.S., Chiu, W., and Mignery, G.A. (2003). Structure of the type 1 inositol 1,4,5-trisphosphate receptor revealed by electron cryomicroscopy. J Biol Chem 278, 21319-21322.
• Ludtke, S.J., and Chiu, W. (2003). Focal pair merging for contrast enhancement of single particles. J Struct Biol 144, 73-78.
• Ludtke, S.J., Nason, L., Tu, H., Peng, L., and Chiu, W. (2003). Object oriented database and electronic notebook for transmission electron microscopy. Microsc Microanal 9, 556-565.
• Serysheva, II, Ludtke, S.J., Baker, M.R., Chiu, W., and Hamilton, S.L. (2002). Structure of the voltage-gated L-type Ca2+ channel by electron cryomicroscopy. Proc Natl Acad Sci U S A 99, 10370-10375.
• Ludtke, S.J., and Chiu, W. (2002). Image restoration in sets of noisy electron micrographs. In IEEE International Symposium on Biomedical Imaging. pp. WA-SS-2.2, IEEE: Washington, D.C.
• Brink, J., Ludtke, S.J., Yang, C.Y., Gu, Z.W., Wakil, S.J., and Chiu, W. (2002). Quaternary structure of human fatty acid synthase by electron cryomicroscopy. Proc Natl Acad Sci U S A 99, 138-143.
• Baker, M.L., Serysheva, II, Sencer, S., Wu, Y., Ludtke, S.J., Jiang, W., Hamilton, S.L., and Chiu, W. (2002). The skeletal muscle Ca2+ release channel has an oxidoreductase-like domain. Proc Natl Acad Sci U S A 99, 12155-12160.
• Saad, A., Ludtke, S.J., Jakana, J., Rixon, F.J., Tsuruta, H., and Chiu, W. (2001). Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination. J Struct Biol 133, 32-42.
• Ludtke, S.J., and Chiu, W. (2001). Electron micrographs: computer enhancement and use for molecular 3-dimensional reconstruction. In Encyclopedia of Life Sciences, Volume 6. (London: Nature Publishing Group), pp. 212-217.
• Ludtke, S.J., and Chiu, W. (2001). Editorial: Special Issue on Single Particle Processing. J Struct Biol 133, 89.
• Ludtke, S.J., Jakana, J., Song, J.L., Chuang, D.T., and Chiu, W. (2001). A 11.5 A single particle reconstruction of GroEL using EMAN. J Mol Biol 314, 253-262.
• Jiang, W., Baker, M.L., Ludtke, S.J., and Chiu, W. (2001). Bridging the information gap: computational tools for intermediate resolution structure interpretation. J Mol Biol 308, 1033-1044.
• Ludtke, S.J., Baldwin, P.R., and Chiu, W. (1999). EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 128, 82-97.

Membrane Peptides

• Heller, W.T., He, K., Ludtke, S.J., Harroun, T.A., and Huang, H.W. (1997). Effect of changing the size of lipid headgroup on peptide insertion into membranes. Biophys J 73, 239-244.
• Ludtke, S.J., He, K., Heller, W.T., Harroun, T.A., Yang, L., and Huang, H.W. (1996). Membrane pores induced by magainin. Biochemistry 35, 13723-13728.
• He, K., Ludtke, S.J., Worcester, D.L., and Huang, H.W. (1996). Neutron scattering in the plane of membranes: structure of alamethicin pores. Biophys J 70, 2659-2666.
• He, K., Ludtke, S.J., Heller, W.T., and Huang, H.W. (1996). Mechanism of alamethicin insertion into lipid bilayers. Biophys J 71, 2669-2679.
• Wu, Y., He, K., Ludtke, S.J., and Huang, H.W. (1995). X-ray diffraction study of lipid bilayer membranes interacting with amphiphilic helical peptides: diphytanoyl phosphatidylcholine with alamethicin at low concentrations. Biophys J 68, 2361-2369.
• Ludtke, S., He, K., and Huang, H. (1995). Membrane thinning caused by magainin 2. Biochemistry 34, 16764-16769.
• Huang, H.W., He, K., Heller, W.T., and Ludtke, S.J. eds. (1995). Interation of Lipid Bilayer Membranes with Amphiphilic Helical Peptides in Short and Long Chains at Interfaces (Paris, France).
• He, K., Ludtke, S.J., Huang, H.W., and Worcester, D.L. (1995). Antimicrobial peptide pores in membranes detected by neutron in-plane scattering. Biochemistry 34, 15614-15618.
• Ludtke, S.J., He, K., Wu, Y., and Huang, H.W. (1994). Cooperative membrane insertion of magainin correlated with its cytolytic activity. Biochim Biophys Acta 1190, 181-184.
• He, K., Ludtke, S.J., Wu, Y., Huang, H.W., Andersen, O.S., Greathouse, D., and Koeppe, R.E., 2nd (1994). Closed state of gramicidin channel detected by X-ray in-plane scattering. Biophys Chem 49, 83-89.
• He, K., Ludtke, S.J., Wu, Y., and Huang, H.W. (1993). X-ray scatteriing in the plane of membrane. Journal de Physique IV 3, 265-270.
• He, K., Ludtke, S.J., Wu, Y., and Huang, H.W. (1993). X-ray scattering with momentum transfer in the plane of membrane. Application to gramicidin organization. Biophys J 64, 157-162.

Other

• Boehm, F., Bonvin, E., Hatamian, S., Herikson, H., Ludtke, S.J., and van Bladel, K. (1991). A large, low-energy neutrino detector for neutrino oscillations and supernovae watch. Nuclear Instruments and Methods in Physics Research A300, 395-402.

Open-source Software Development

Current Projects:

EMAN Complete 3D single particle reconstruction package. (stable v1.70)

EMAN2 Refactoring of the EMAN core, focusing on Python scripting support. (pre-alpha)

EMEN Electron Microscopy Electronic Notebook. A Zope-based electronic notebook currently storing over 5 terabytes of image data and metadata at the NCMI. (stable)

Stable but no longer developed:

emtool A xforms-based program for interactve image processing of electron micrographs. Useful, but most of its functionality has been subsumed by EMAN.

empgm Nongraphical electron microscopy image format converter. (also see proc2d in EMAN)

tld2mrc Converts Zeiss .tld files to MRC format.

NXplotNd A multidimensional plotting and data analysis program (NeXTStep ONLY)

NXPlot3d 3.1 An easy to use 3d plotting program (data and functions) (NeXTStep ONLY)

MolViewer 0.92 A molecule viewing and manipulation program (NeXTStep ONLY)

Houston Interactive Restaurant Database (discontinued) A database of the restaurants in the Houston area with real time searching and user provided data with an interactive Java client with map.

To contact me: