News and Publications
TSRI Scientific Report 1998-1999
The capsid structure of the double-stranded DNA bacteriophage HK97 as determined by x-ray crystallography. The 420 identical protein subunits (represented as tubes) form a capsid that is 650 Å in diameter but only 25 Å thick. This thin shell is stabilized by 420 covalent intersubunit cross-links between lysine 169 and asparagine 356 (CPK spheres). These cross-links form autocatalytically as the last step in the complex process of particle maturation. The subunits interlock via circular concatamers, or "chain mail," in which 5 subunits surrounding the pentamer form a "superpentamer" (turquoise) or 6 subunits surrounding the hexamer form a "superhexamer" (various colors) of covalently bonded neighbors. These superhexamers and superpentamers interloop in a chain-link organization that covalently interlocks the entire phage capsid. In the background are electron micrographs of infectious phage particles, with the capsid x-ray structure superimposed. HK97 infects an Escherichia coli cell when the long, noncontractile tail of the phage binds specifically to the cell surface and the 40 kbp of genomic DNA inside the capsid is injected directly into the cell through the tail. The crystal structure was determined by William R. Wikoff, Ph.D., and Lars Liljas, Ph.D., in the laboratory of John E. Johnson, Ph.D., with collaborators Robert Duda, Ph.D., and Roger Hendrix, Ph.D., at the University of Pittsburgh. The image was created by Dr. Wikoff.
The genetic integrity of cells depends on the DNA base excision repair pathway, which is responsible for recognizing and removing damaged bases in DNA. A key enzyme in this pathway is endonuclease IV, and this past year a team of researchers led by John Tainer, Ph.D., solved high-resolution 3-dimensional structures of this enzyme both alone and in complex with damaged DNA. These structures revealed that endonuclease IV (dark blue ribbons) recognizes damaged DNA (white tubes, with colored polar atoms) by inserting protein side chains into the DNA minor groove to promote double-nucleotide flipping that bends the DNA double helix by 90°. This work helps to establish that deformability of damaged DNA is a general model for repair enzyme-DNA molecular recognition events.
Orthogonal, stereo views of the 3-dimensional density map of human AQP1 water channel determined by electron cryo-crystallography of 2-dimensional crystals of the channel generated in synthetic lipid bilayers. Top panel, Density map at an in-plane resolution of 4 Å shows a monomer and parts of adjacent monomers viewed perpendicular to the bilayer. The monomer, composed of 6 tilted a-helices, encloses the water-selective channel. Bottom panel, In a view parallel to the bilayer, the solvent-accessible region within a monomer is represented as a light-gray-colored, partially transparent volume. The vestibular shape, broader at the cytoplasmic (bottom) and the extracellular (top) sides, narrows down to approximately 6 Å near the center of the bilayer where the water-selective barrier is presumably located. Scale bar = 10 Å. Work done in the laboratory of A.K. Mitra, Ph.D. Image by M. Pique, G. Ren, and A.K. Mitra.
The two sets of images above are stereograms which can be viewed without special glasses using a convergent or cross-eyed viewing technique to obtain a 3D picture. Many people find this difficult to do the first time. You have to focus on a point which is different from where you are looking; this is known as "de-coupling" your vision process.
To see these images in 3D try the following method:
1) Look at one set of images (stereo pairs) and cross your eyes slightly. You should see 4 images.
2) Continue to cross your eyes slowly so that the 2 images in the center come together or converge. This center image will be a 3D image. It will lie between the 2 flat images which can be ignored.
3) The 3D image will be blurred at first, but keep trying to hold the stereo pair together while you focus. The longer you can hold it, the more time your eyes will have to adjust their focus. Eventually the 2 images in the center will lock together as your mind and eyes view it as a 3D image.