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Color illustrations
Clifford A. Pickover
DNA and protein tetragrams: Biological sequences as tetrahedral movements Color Plate 1. DNA Tetragram. Superposition of the viral harvey murine sarcoma DNA (bottom) and Kirsten sarcoma DNA (top). This Kirsten gene shows an obvious direction trend with several visually distinct (GC) regions. The sequences may be thought of as starting at the center of the large sphere and running outward (5’ to 3’ end). The scheme for coloration of the spheres and axes is: G, red; C, yellow; A, green; and T, blue.
(4
K4
Color Plate 2. Amino acid tetragram for amino acid sequences bovine alpha-lactalbumin, a milk protein (c).
of hen egg white
rsozyme (a), human lysozyme
(b), and
Color Plate 3. An evolutionary sequence of amino acid tetragrams for six different organisms (see text). The origin of each tetragram is offset slightly to facilitate visualization of the different sequences.
J. Mol. Graphics,
1992, Vol. 10, March
17
Paul W. Chun and Wou Seok Jou
Molecular conformation of ubiquitinated structures and the implications for regulatory function
Color Plate 1. The X-K linkage model, where C-terminal glycine is attached through the N-terminus of a-amino group of an X-hexapeptide of the acceptor molecule. X is the N-terminus aNH2 group of glutamic acid residue X-El-H2-K3-G4-K5V6. A second Ubiquitin (Ub) is attached through e-amino group of lysine (K5) of X-hexapeptide.
The full sequence of Ub in single-letter
code is shown below
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDVNIQKESTLHLVLRLRGG A single Ub molecule attached to the X-hexapeptide in different locations for the X-K and K-K linkage model was energy minimized by 1000 interactions, which corresponds to 60,000 energy evaluation counts. Each time an additional Ub molecule was added, the torsion angles were scanned to relieve steric interactions and to seek a portion in which there is no van der Waals contact between either side of the bond. Additional energy minimization of 3000 iterations (or 18,000 energy evaluation counts) was run whenever two separate Ub molecules were joined.15 (A) Before energy minimization. This ribbon model shows the two Ub molecules attached through an X-hexapeptide on a linear plane, with the second molecule, attached at the lyss position (K5), at a 90” angle from that plane. (B) After energy minimization. The two Ub molecules are on the same linear plane, with a 180”-turn between the first and second molecule.
Color Plate 2. The X-K linkage model after energy -. minimization. amino group of the X-val, hexapeptide:
(Uh,IUQPL
of the a-amino ~- LRFG
J. Mol. Graphics,
1992, Vol. 10, March
group of the Xarg,-hexapeptide: “dl,.
X-~r~,~h,\,-l~\,-~ly,
The Ub hexapeptide was energy minimized as described additional ubiquitin molecule was added, and additional reference notes. 18
of the (Y-
“‘Il. -Vsl,~h,\l-ly\,~ply, lyr,.GGRLLFOM 1 (“b,
,“h, (B) The Ub is attached through the N-terminus
(A) The Ub is attached through the N-terminus
GGRL ~~~~LFQM ’I>\,- m
l”b,
in Color Plate 1, but the torsion angles were not scanned. An energy minimization was run. Energy levels are shown in the
Color Plate 3. Effect of multi-ubiquitination on the X-K linkage model. (A) A ribbon model of four Ub molecules attached through the E-amino groups of lysine (KY) of an X-hexapeptide, before and after energy minimization. fB) A ribbon model of four Ub mofecufes attached through the N-terminus of an X-hexa~ptide to which two additional Ub molecules are attached at the K5 position, before and after energy minimization.
Color Plate 4. Effect of multi-ubiquitina~ion on theX-K linkage model. Two Ub molecules are joined through anX-hexapeptide and four additional Ub molecules are joined to the acceptor bexa~ptide at the K3 position.
J. Mol. Graphics, 1992, Vol. 10, March
19
Color Plate 5. The K-K linkage model, in which Ub is attached directly to the e-amino group of lysine (K3) of the acceptor peptide. A second Ub is attached through e-amino group of lysine (K5) of the acceptor molecule. (A) Before energy minimization, this ribbon model shows the two Ub molecules attached through the e-amino group of lysine (K3) on a circular hexapeptide plane, with the second molecule attached at the Lys, position (KS) at a 135” angle from that plane, resulting in a confo~ational relaxation in the P-pleated sheets and P-turns and a distinctly extended o-helix. (B) After energy minimization, the two Ub molecules are on the same plane in the u-shaped semicircular formation with a noticeable compaction of the two molecules. 76 I 48 (Uhl MQLF K LRGG y
x~~~~~~i,,, 7h
Before energy minfmlzatlon
After energyminimizatbn
Color Plate 6. The effect of multi-ubiquitination through internal lysine-48 (K48) of the adjacent Ub molecule in an acceptor hexapeptide on the K-K linkage model. (A) Three Ub molecules (in K-K linkage) are attached through the e-amino group of lysine (K3) of the hexapeptide, to which two additional Ub molecules are attached at K.5, before and after energy minimization. (Bf Four Ub molecules (in K-K linkage) are attached through the internal lysine-48 of the adjacent Ub without hexapeptide. The carboxyl terminus of Ub is located approximately at 90” relative to the lysine-48 (K48) of an adjacent Ub’,‘.
D.A. Kuznetsov and H.A. Lim
VisiCoor: A simple program for visualization of proteins Color Plate 1. Dipeptide Tyr-Pro covered by sticks. Edges on sticks help the viewer to estimate the direction of bonds and the torsion angles between atoms.
Color Plate 2. Main chain of the protein flavodoxin (4FXN). Four a-helices are covered by van der Waals spheres while other substructures (both P-sheet and irregular) are represented by sticks. The /3 sheet is painted in orange, other atoms have CPK colors. The image was created by the following steps: 1) the a-helix criterion was chosen and a class with this criterion was built (passage through five menu items); 2) the classified atoms were covered by the van der Waals spheres (two menu items); 3) the class was inverted (three menu items); 4) the classified atoms were covered by the sticks (two menu items); 5) the P-sheet criterion was chosen and a class with this criterion was built (five menu items); 6) the classified atoms were painted in orange (two menu items). The plot helps one to learn the mutual arrangement of a-helices and P-sheets.
Color Plate 3. Main chain of the Bence-Jones protein (2RHE). The structure of the protein includes two large P-sheets represented by violet van der Waals spheres. The irregular structures are covered by orange sticks.
J. Mol. Graphics,
1992, Vol. 10, March
21
Color Plate 4. Main chain of the protein plastocyanin (1PCY). The frame of the structure consists of the large eight-stranded P-sheet (the so-called P-barrel), which is represented by violet van der Waals spheres. The irregular structure is covered by orange sticks.
Color Plate 5. Another
view of the protein
plastocyanin
C-end-of the protein) while the hydrophilic main chain and polar side chains are represented by sticks. Two criteria were chosen to define exactly only hydrophobic side chains: 1) hydrophobic residues; and 2) reversed main-chain criterion. The plot helps in investigating the hydrophobic core, which is located inside the P-barrel structure.
Color Plate 6. Active site of the protein ribonuclease (lRN3). The atoms that are within the intersection of the protein globule with the two spheres centered on the ND1 of HIS 119 and the CG of PHE 120, respectively, are represented by sticks; other atoms are covered by balls. The user inputs the number of atoms and the radius of spheres at the popup menu prompts, when the criterion of vicinity to an atom is selected. The mouse cursor points to CG of PHE 120.
22
J. Mol. Graphics,
1992, Vol. 10, March
David C. Turner and Bruce Paul Gaber
A crystallographic molecular lattice builder applied to model lipid bilayers b
a
Color Plate 1. a) Monolayers of DMPC apposed at the head Within the lipid the carbon atoms are green, nitrogen atoms red. The balls represent 0.4 of the van der Waals radii; b) true van der Waals radii. The colors lighten as the atoms and 6.
a
groups showing the waters of crystallization as magenta spheres, are blue, phosphorous atoms are yellow, and oxygen atoms are bilayer of DMPC shown in perspective; the balls represent the appear closer to the viewer. Data are taken from references 4
b
Color Plate 2. a) Bali-and-stick projection of the OMPC mofecuIe on the a-e plane showing the herringbone packing; b) perspective view of the b-e plane; the molecules are seen to stitch in and out of the pfane. Data are taken from reference 7.
Color Plate 3. Model bilayer of DOT%! shown in perspective mode with NanoVision. This is a pseudo structure that could he used as a starting point for molecufar simulations.
J. Mol. Graphics,
1992, Vol. 10, March
23
Leif Laaksonen
A graphics program for the analysis and display of molecular dynamics trajectories
Color Plate 1. Snapshot from the CBH-I simulation showing the distance from the oxygen in the tyrosine 16 to the oxygen of a nearby water. The whole distance history can be seen from the diagram. A yellow ‘ + ’ sign indicates the place in the time series.
Color Plate 2. The CBH-I tail is colored according to the force (CHARMm force field) acting on the atoms. Blue is high and red is low force. The color scale can be seen on the left.
24
J. Mol. Graphics,
1992, Vol. 10, March
DNA and protein tetragrams: Biological sequences as tetrahedral movements Color Plate 1. DNA Tetragram. Superposition of the viral harvey murine sarcoma DNA (bottom) and Kirsten sarcoma DNA (top). This Kirsten gene shows an obvious direction trend with several visually distinct (GC) regions. The sequences may be thought of as starting at the center of the large sphere and running outward (5’ to 3’ end). The scheme for coloration of the spheres and axes is: G, red; C, yellow; A, green; and T, blue.
(4
K4
Color Plate 2. Amino acid tetragram for amino acid sequences bovine alpha-lactalbumin, a milk protein (c).
of hen egg white
rsozyme (a), human lysozyme
(b), and
Color Plate 3. An evolutionary sequence of amino acid tetragrams for six different organisms (see text). The origin of each tetragram is offset slightly to facilitate visualization of the different sequences.
J. Mol. Graphics,
1992, Vol. 10, March
17
Paul W. Chun and Wou Seok Jou
Molecular conformation of ubiquitinated structures and the implications for regulatory function
Color Plate 1. The X-K linkage model, where C-terminal glycine is attached through the N-terminus of a-amino group of an X-hexapeptide of the acceptor molecule. X is the N-terminus aNH2 group of glutamic acid residue X-El-H2-K3-G4-K5V6. A second Ubiquitin (Ub) is attached through e-amino group of lysine (K5) of X-hexapeptide.
The full sequence of Ub in single-letter
code is shown below
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDVNIQKESTLHLVLRLRGG A single Ub molecule attached to the X-hexapeptide in different locations for the X-K and K-K linkage model was energy minimized by 1000 interactions, which corresponds to 60,000 energy evaluation counts. Each time an additional Ub molecule was added, the torsion angles were scanned to relieve steric interactions and to seek a portion in which there is no van der Waals contact between either side of the bond. Additional energy minimization of 3000 iterations (or 18,000 energy evaluation counts) was run whenever two separate Ub molecules were joined.15 (A) Before energy minimization. This ribbon model shows the two Ub molecules attached through an X-hexapeptide on a linear plane, with the second molecule, attached at the lyss position (K5), at a 90” angle from that plane. (B) After energy minimization. The two Ub molecules are on the same linear plane, with a 180”-turn between the first and second molecule.
Color Plate 2. The X-K linkage model after energy -. minimization. amino group of the X-val, hexapeptide:
(Uh,IUQPL
of the a-amino ~- LRFG
J. Mol. Graphics,
1992, Vol. 10, March
group of the Xarg,-hexapeptide: “dl,.
X-~r~,~h,\,-l~\,-~ly,
The Ub hexapeptide was energy minimized as described additional ubiquitin molecule was added, and additional reference notes. 18
of the (Y-
“‘Il. -Vsl,~h,\l-ly\,~ply, lyr,.GGRLLFOM 1 (“b,
,“h, (B) The Ub is attached through the N-terminus
(A) The Ub is attached through the N-terminus
GGRL ~~~~LFQM ’I>\,- m
l”b,
in Color Plate 1, but the torsion angles were not scanned. An energy minimization was run. Energy levels are shown in the
Color Plate 3. Effect of multi-ubiquitination on the X-K linkage model. (A) A ribbon model of four Ub molecules attached through the E-amino groups of lysine (KY) of an X-hexapeptide, before and after energy minimization. fB) A ribbon model of four Ub mofecufes attached through the N-terminus of an X-hexa~ptide to which two additional Ub molecules are attached at the K5 position, before and after energy minimization.
Color Plate 4. Effect of multi-ubiquitina~ion on theX-K linkage model. Two Ub molecules are joined through anX-hexapeptide and four additional Ub molecules are joined to the acceptor bexa~ptide at the K3 position.
J. Mol. Graphics, 1992, Vol. 10, March
19
Color Plate 5. The K-K linkage model, in which Ub is attached directly to the e-amino group of lysine (K3) of the acceptor peptide. A second Ub is attached through e-amino group of lysine (K5) of the acceptor molecule. (A) Before energy minimization, this ribbon model shows the two Ub molecules attached through the e-amino group of lysine (K3) on a circular hexapeptide plane, with the second molecule attached at the Lys, position (KS) at a 135” angle from that plane, resulting in a confo~ational relaxation in the P-pleated sheets and P-turns and a distinctly extended o-helix. (B) After energy minimization, the two Ub molecules are on the same plane in the u-shaped semicircular formation with a noticeable compaction of the two molecules. 76 I 48 (Uhl MQLF K LRGG y
x~~~~~~i,,, 7h
Before energy minfmlzatlon
After energyminimizatbn
Color Plate 6. The effect of multi-ubiquitination through internal lysine-48 (K48) of the adjacent Ub molecule in an acceptor hexapeptide on the K-K linkage model. (A) Three Ub molecules (in K-K linkage) are attached through the e-amino group of lysine (K3) of the hexapeptide, to which two additional Ub molecules are attached at K.5, before and after energy minimization. (Bf Four Ub molecules (in K-K linkage) are attached through the internal lysine-48 of the adjacent Ub without hexapeptide. The carboxyl terminus of Ub is located approximately at 90” relative to the lysine-48 (K48) of an adjacent Ub’,‘.
D.A. Kuznetsov and H.A. Lim
VisiCoor: A simple program for visualization of proteins Color Plate 1. Dipeptide Tyr-Pro covered by sticks. Edges on sticks help the viewer to estimate the direction of bonds and the torsion angles between atoms.
Color Plate 2. Main chain of the protein flavodoxin (4FXN). Four a-helices are covered by van der Waals spheres while other substructures (both P-sheet and irregular) are represented by sticks. The /3 sheet is painted in orange, other atoms have CPK colors. The image was created by the following steps: 1) the a-helix criterion was chosen and a class with this criterion was built (passage through five menu items); 2) the classified atoms were covered by the van der Waals spheres (two menu items); 3) the class was inverted (three menu items); 4) the classified atoms were covered by the sticks (two menu items); 5) the P-sheet criterion was chosen and a class with this criterion was built (five menu items); 6) the classified atoms were painted in orange (two menu items). The plot helps one to learn the mutual arrangement of a-helices and P-sheets.
Color Plate 3. Main chain of the Bence-Jones protein (2RHE). The structure of the protein includes two large P-sheets represented by violet van der Waals spheres. The irregular structures are covered by orange sticks.
J. Mol. Graphics,
1992, Vol. 10, March
21
Color Plate 4. Main chain of the protein plastocyanin (1PCY). The frame of the structure consists of the large eight-stranded P-sheet (the so-called P-barrel), which is represented by violet van der Waals spheres. The irregular structure is covered by orange sticks.
Color Plate 5. Another
view of the protein
plastocyanin
C-end-of the protein) while the hydrophilic main chain and polar side chains are represented by sticks. Two criteria were chosen to define exactly only hydrophobic side chains: 1) hydrophobic residues; and 2) reversed main-chain criterion. The plot helps in investigating the hydrophobic core, which is located inside the P-barrel structure.
Color Plate 6. Active site of the protein ribonuclease (lRN3). The atoms that are within the intersection of the protein globule with the two spheres centered on the ND1 of HIS 119 and the CG of PHE 120, respectively, are represented by sticks; other atoms are covered by balls. The user inputs the number of atoms and the radius of spheres at the popup menu prompts, when the criterion of vicinity to an atom is selected. The mouse cursor points to CG of PHE 120.
22
J. Mol. Graphics,
1992, Vol. 10, March
David C. Turner and Bruce Paul Gaber
A crystallographic molecular lattice builder applied to model lipid bilayers b
a
Color Plate 1. a) Monolayers of DMPC apposed at the head Within the lipid the carbon atoms are green, nitrogen atoms red. The balls represent 0.4 of the van der Waals radii; b) true van der Waals radii. The colors lighten as the atoms and 6.
a
groups showing the waters of crystallization as magenta spheres, are blue, phosphorous atoms are yellow, and oxygen atoms are bilayer of DMPC shown in perspective; the balls represent the appear closer to the viewer. Data are taken from references 4
b
Color Plate 2. a) Bali-and-stick projection of the OMPC mofecuIe on the a-e plane showing the herringbone packing; b) perspective view of the b-e plane; the molecules are seen to stitch in and out of the pfane. Data are taken from reference 7.
Color Plate 3. Model bilayer of DOT%! shown in perspective mode with NanoVision. This is a pseudo structure that could he used as a starting point for molecufar simulations.
J. Mol. Graphics,
1992, Vol. 10, March
23
Leif Laaksonen
A graphics program for the analysis and display of molecular dynamics trajectories
Color Plate 1. Snapshot from the CBH-I simulation showing the distance from the oxygen in the tyrosine 16 to the oxygen of a nearby water. The whole distance history can be seen from the diagram. A yellow ‘ + ’ sign indicates the place in the time series.
Color Plate 2. The CBH-I tail is colored according to the force (CHARMm force field) acting on the atoms. Blue is high and red is low force. The color scale can be seen on the left.
24
J. Mol. Graphics,
1992, Vol. 10, March