Molecular Modeling Course 99

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Time: Thursdays, 12:45-2:45pm

Location: 1003 Main Building

Kinemage (``Kinetic Images'') Tutorial

Tamar Schlick

The kinemage program created by Dave and Jane Richardson of Duke University is a wonderful way to study protein structure. Their program offers instructive sets of biomolecular images that can be manipulated in various ways so as to understand the three-dimensional complexity and variability of biomolecular systems.

Below are instructions on how to use the kinemage tutorial. Basically, you will need to first download two types of files: the driver program that manipulates kinemage files and the data files themselves. The driver program can be taken for Mac, PC, SGI machines, and other computers. The instructions below refer to SGI platforms, but you will simply need to transfer a different driver file for another machine; file names are self-explanatory. You can obtain some general information on kinemage through the Richardsons' web site:

The instructions below assume you have basic knowledge of transferring files via ftp. If you do not, read the online manual (type: man ftp). To run the kinemage programs using the SGI driver, you will need an SGI machine with SGI operating system version 6.2 or higher.

  1. Transfer MAGE and kinemage files
    1. FTP to the resource site by typing at the Unix command line Log in as anonymous. You will now be receiving ftp prompts as:
    2. Go to the appropriate subdirectory by typing at the ftp command line:
      cd UNIXprograms
    3. Specify binary mode of transfer on the ftp command line as follows:
      (The file you transfer is an executable file, so an ASCII (text) transfer mode will cause error when you want to run the program).
    4. Now get the kinemage driver program:
      get MAGE_5.30_990119.SGI
      (To ensure correct file transfer, it is a good idea to compare the size of the retrieved file with that of the original).
    5. Now scroll to a different subdirectory where the kinemage input files reside:
      cd ../KINfiles
    6. Check the list of available files by typing:
      You should see several files, including ProTour1.kin, ProTour2.kin, ProTour3.kin, ProTour4.kin, ProTour5.kin, ProTour6.kin, ProTour7.kin, ProTour9.kin, and NATour1.kin.
    7. Retrieve each of the above files in turn by using the ftp command:
      where represents one of the above titles. Apparently, the remote server does not support the multiple retrieving mode at the time of this writing.
    8. Exitfrom from ftp by typing:

      Check that you have all the necessary files by typing the Unix commands
      ls *.kin

      and then

      ls MAGE*

  2. Run the kinemage program

    1. In your Unix command line, change the mode of the file MAGE_5.30_990119.SGI to executable by typing:
      chmod +x MAGE_5.30_990119.SGI

    2. Start the program by tying:

      You will see four windows, with the front window (of title MAGE GRAPHICS) awaiting your response. Press the proceed button to hide the front window. The two smaller windows may be behind the main one; try move the main window aside so that the others, with titles MAGE TEXT and MAGE CAPTION, will be in sight.

    3. To use kinemages to study protein structures, pull down the main window's file menu, and choose the open new file... to start a session. You can select (or type in the name) of one of your transferred .kin files, and then press the OK button. The main window will display a picture of a biomolecule, while the MAGE TEXT window will provide explanatory text about the system. The MAGE CAPTION window shows the information of the current kinemage in view. There are typically several kinemages in the same .kin file.

    4. To view another kinemage in the same file, select Next or Choose from the Kinemage menu.

    5. To manipulate the image, rotate it by moving the mouse with the left button pressed. You can also click on the boxes on the right side to turn off/on various displays or markers. Read the help text by clicking on the Help Mage menu and choosing a topic.

Content of MAGE Files

Below is a brief synopsis of the tutorial .kin files for easy reference; descriptions are taken straight from MAGE TEXT. I suggest the following order of study.

Protein Classification and Motifs

  1. ProTour7.kin: Major Protein Folding Motifs ( tex2html_wrap_inline109 , tex2html_wrap_inline111 , tex2html_wrap_inline109 / tex2html_wrap_inline111 )

    Each of these kinemages shows ribbon-diagrams (one-strand, smooth splines along the Calpha backbone) for a sample of protein structures typical of one of the major categories of tertiary structure. In each kinemage, click on the ``ANIMATE" button to switch among the example proteins. The ribbons are depth-cued by line width, secondary-structure features are color-coded, prosthetic groups are shown, and the N- and C-termini are labeled. Clicking on a point along the ribbon will display the residue name and number at the bottom left of the screen. Drag slowly with the mouse to rotate the molecule, for a 3-D perception, or hit the ``s" key on the keyboard to toggle side-by-side stereo on and off. (NOTE: use the ANIMATE button to switch among these examples since this invokes special recentered views.)

    Kin.1- All-Alpha structures: myohemerythrin, cytochrome b562, & calbindin
    Kin.2- Parallel Alpha/Beta structures: flavodoxin & triose P isomerase
    Kin.3- Antiparallel Beta structures: Strep. subtilisin inhibitor, trypsin d2, & STNV
    Kin.4- Small Irregular structures: BPTI, crambin, & cytochrome c3

  2. ProTour1.kin: tex2html_wrap_inline111 Sheet Motif

    The doubly-wound parallel beta sheet, a subset of the Parallel Alpha/Beta type of tertiary structure, is the commonest folding pattern found in the known protein structures. This ``fold" is also known as the ``nucleotide-binding domain", because most of them bind a mononucleotide (such as FMN) or a dinucleotide (such as NAD) near the middle of one end of the beta sheet. This month's Protein Tourist illustrates the main features of this protein ``fold", to be used for general information purposes or for teaching. No further permission is needed for educational use of kinemages from Protein Tourist or Demo files.

    Kin.1 - A parallel beta sheet, with H-bonds
    Kin.2 - Right-handedness of crossover connections
    Kin.3 - LDH domain 1, with animation of the ``double winding"
    Kin.4 - ADH domain 2, another classic doubly-wound sheet
    Kin.5 - DHFR, a less regular doubly-wound sheet
    Kin.6 - Nucleotide binding in LDH, with helix dipole and moving loop
    Kin.7 - Domain organization in LDH

  3. ProTour2.kin: Leucine Zipper

    A motif known as the ``leucine zipper" mediates dimerization of the bZIP and bHLH-ZIP classes of transcription factors. Leu zipper sequences are characterized by a sequence of 30 or 40 helix-tolerating amino acids with Leu every seven residues. Leucine zipper peptides form dimers of parallel helices proposed to be similar to coiled coils common in much longer alpha-fibrous proteins. A recent high-resolution x-ray structure of a synthetic, 33-residue fragment of the yeast transcription factor GCN4 confirms that the leucine zipper forms a coiled coil, and illustrates interactions that mediate dimerization. This Protein Tourist allows readers to explore the GCN4 leucine zipper structure.

    Kin.1 - Tropomyosin Calphas: a long coiled-coil in a fibrous protein
    Kin.2 - A short, distorted coiled coil in the dimer interface of CAP protein
    Kin.3 - GCN4 leucine zipper peptide: a high-resolution coiled-coil structure
    Kin.4 - Salt bridges around the outside of the zipper hydrophobic core
    Kin.5 - Asymmetrical arrangement of Asn 16

  4. ProTour4.kin: Disuphide-Bond-Rich Proteins

    Small SS-rich, C-centered overhand structures:
    Kin.1 - Cellobiohydrolase C-terminal domain: overhand topology and C-C beta hairpin
    Kin.2 - Potato carboxypeptidase inhibitor: very small SS-rich
    Kin.3 - Scorpion neurotoxin
    Kin.4 - Closeup of glycine roles, in scorpion toxin

    Small SS-rich, N-centered overhands and others:
    Kin.5 - Ovomucoid serine protease inhibitor: N-centered topology
    Kin.6 - Wheat germ agglutinin domain
    Kin.7 - Hirudin: up & down topology, with 3-SS core Small metal-rich structures
    Kin.8 - Rubredoxin: one non-heme Fe
    Kin.9 - Ferredoxin (P. aer.): two Fe4S4 clusters
    Kin.10- Cytochrome C3: 4 hemes
    Kin.11- Metallothionein domain 2: 4 Cd sites in 31 residues Small proteins with neither disulfides nor metals
    Kin.12- Immunoglobulin-binding domain of Strep. protein G

    Specific Proteins

  5. ProTour3.kin: tex2html_wrap_inline119 Repressor

    Kin.1 - Overview, with Lambda repressor Calphas and virtual-bond DNA
    Kin.2 - DNA, for consensus half-operator sequence, with bases color-coded
    Kin.3 - Detail of sequence-specific interactions with bases in one major groove
    Kin.4 - Non-specific interactions with phosphate backbone

  6. ProTour5.kin: Carboxypeptidase

    Kin.1 - Overview of the 3-D structure of carboxypeptidase A
    Kin.2 - Carboxypeptidase active site motions on substrate binding
    Kin.3 - Structure of a tetrahedral transition-state analog at the active site, animated
    Kin.4 - Potato carboxypeptidase inhibitor, as bound to CPA Thermolysin
    Kin.5 - Thermolysin: overall structure
    Kin.6 - Closeup of ZFpLA bound at thermolysin active site
    Kin.7 - Comparison of thermolysin and carboxypeptidase, Calphas & active sites

  7. ProTour6.kin: Inhibitor Complexes

    Kin.1 - Thrombin, with backbone, Ser-His-Asp-Ser, PPACK inhibitor, and beta barrels
    Kin.2 - Trypsin-BPTI complex: overview of inhibitor binding
    Kin.3 - Trypsin-BPTI complex: detail of active site, with small-probe dot contacts
    Kin.4 - Superposition of trypsin, chymotrypsin, and subtilisin

  8. ProTour9.kin: Pectate Lyase C

    Pectate Lyase C (PelC) has a novel 3-dimensional structure, made up almost entirely of an L-shaped, or triangular, coil of parallel beta sheet. This represents a new major category of protein tertiary-structure, the all-beta parallel category.

    Kin.1 - Pectate Lyase C: buildup of the parallel beta coil, in sequence order
    Kin.2 - PelC: an animated tour of features, on the Calpha backbone
    Kin.3 - Sidechain stacking in the interior of PelC: the Asn ladder


  9. NATour1.kin: B-DNA Oligomers

    Kin.1 -  5'-D( C  G  C  G  A  A  T  T  C  G  C  G)-3', 290 (NDB file: BDL001)
    Kin.2 -  5'-D( C  G  C  A  T  A  T  A  T  G  C  G)-3'                (BDL007) 
    Kin.3 -  5'-D( C  G  C  A  A  G  C  T  G  G  C  G)-3'                (BDL022) 
    Kin.4 -  5'-D( C  G  C  G  (M)A  A  T  T  C  G  C  G)-3'             (BDLB13) 
    Kin.5 -  5'-D( C  G  C  G  A  A  T  T  (BR)C  G  C  G)-3', NETRO SIN (GDLB05)
    Kin.6 -  5'-D( C  G  C  A  A  A  T  T  T  G  C  G)-3', DISTAMYCIN    (GDL003) 
    Kin.7 -  5'-D( C  G  C  G  A  A  T  T  C  G  C  G)-3', BERENIL       (GDL009)
    Kin.8 -  5'-D( C  G  C  G  A  A  T  T  C  G  C  G)-3',4'-6-DIAMIDINE-2-PHENYL

    INDOLE (DAPI) (GDL008)

For further information, contact T. Schlick by email ( phone (998-3116) or fax (995-4152).