Molecular Modeling

Downloaded by 187.39.199.130 on May 16, 2018 | https://pubs.acs.org Publication Date: December 14, 1994 | doi: 10.1021/bk-1994-0576.ap001

These color plates are for Chapter 4.

Color plate 1. Molecular models of FL (top left), FS (top middle), FQ (top right), FP (bottom left) and LP (bottomright),shown asribbonswith the sidechains of the substituted residues displayed. Compact subunits, green; cell attachment site, red.

Color plate 2. Superposition of all the heavy atoms from the alpha carbon of Leu-151 to the amide nitrogen of Arg-154, inclusive, of the FP (blue) and LP (yellow) molecular models. Hydrogen bond, green dashed line.

Kumosinski and Liebman; Molecular Modeling ACS Symposium Series; American Chemical Society: Washington, DC, 1994.


This color plate is for Chapter 7.

Color Plate 3. Energy refined models of from left to right apo lipophorin-III (residues 7 - 156), canine apolipoprotein A-I (residues 72 - 236), human apolipoprotein A-I (residues 73 - 237) and chicken apolipoprotein A-I (residues 72 - 236). Peptide backbones are represented by a double strandedribbon.In the lateral view, only ionizable sidechains are displayed with acidic groups (Glu, Asp) in red and basic groups (Lys, Arg) in blue. In the end-on view only hydrophobic sidechains (Ala, He, Leu, Met, Phe, Tyr, Trp, Val) are displayed in orange.




Color Plate 4. Ribbon tracing of the polypeptide backbone of the theoretical working model for sTF. The four tryptophan residues (14, 25, 45, and 158) are shown as well as the subtilisin cleavage between residues 86 and 87.

Color Plate 5. Line tracing of the backbone of the working model for sTF showing side chains. Kumosinski and Liebman; Molecular Modeling ACS Symposium Series; American Chemical Society: Washington, DC, 1994.


2

Color plate 6. Model of αΒ backbone with added sidechains. Color code: yellow, backbone; red and purple, negative and positive chargée! sidechains, respectively; green, hydrophobic sidechains.


9

ο

Ή. ET

Kumosinski and Liebman; Molecular Modeling ACS Symposium Series; American Chemical Society: Washington, DC, 1994. 2

2

Color plate 7. "Working" model of the otP^ and aB complex. The backbone of aA^ (left) and aB (right) is orange and yellow, respectively.


ο *-ι

9 Ή

ES*

Ή. ST

8 δ*


Color plate 8. An attempt to superimpose the Greek key folding pattern and /^-pleated sheet secondary structure of bovine 7-crystallin (left) on the aA primary structure resulted in a nonsense molecule (right). Color code: white, backbone of respective molecules; blue, proline residues; red and purple, negative and positive charged sidechains, respectively; green, hydrophobic sidechains.



Color Plate 9. Telopeptide binding site region in type II collagen microfibril. Glycine 1 position is labelled "Gly I." Negative, positive and non-polar amino acid sidechains are colored red, blue and orange, respectively.



Color Plate 10. Type Π collagen microfibril space-filling models. Top. Backbone features of model indicating the boundaries of two overlap and one gap region, with each triple helix labelled with a different color; upper middle. Hydroxyproline distribution (colored yellow) within the microfibril; lower middle. Proline distribution (colored blue) within the microfibril; bottom. Combined proline and hydroxyproline distributions.

Imino Acid Distribution in Type II Microfibril


Ό

Ο sr

Ή. ET



Color Plate No. 11. 120-residue γ spiral resulting from the 6-residue repeating sequence prior to energy minimization and dynamics calculations. Side view of spiral with backbone represented by aribbonstructure and hydrogen bonds shown as dashed lines. Only glutamine side chains shown.




Color Plate No. 12. Structure as in Color Plate No. 11, but after 30 ps of dynamics calculations.




MYGLOBIN DDAB 48

Color Plate 13. Top view of model of Mb-DDAB after 40 ps dynamics. Mb histidine residues unprotonated. Only amino acid residues shown for Mb in the center of the 48-DDAB bilayer (blue). For Mb, purple = positive; red = negative; green = hydrophobic; yellow = heme.




MYGLOBIN HIP DDAB 48

Color Plate 14. Top view of model of Mb-DDAB after 40 ps dynamics. Mb histidine residues protonated. Only amino acid residues shown for Mb in the center of a 48-DDAB bilayer (blue). For Mb, purple = positive; red = negative; green = hydrophobic; yellow = heme.



Tnis color plate is for Chapter 17.

+

COLOR PLATE 15. Idealized 3D Model of U (nH 0)Cl" tetramer clusters in concentrated aqueous solutions of lithium chloride at 298 K. 2



0.1

n m


H^-—I

COLOR PLATE 16. Molecular model of Li (nH 0)Cl~, water-bridged ion 2

clusters in glasses at 100 K, derived from pulsed H NMR data.




Proline 8 Water 4; t = 50 ps COLOR PLATE 17. The configuration of water and proline molecules are shown after 50 ps from the start of simulation.




Color Plate 18. A side view of one protomer, shown as a solid ribbon,with the external side of the capsid at the top and the internal side at the bottom. Residues 132-134 and 157-159 of VP1 at the base of the immunodominant loop are shown in violet. VP1, blue; VP2, green; VP3, red; VP4, yellow.




Color Plate 19. Energy minimized three dimensional molecular model of a -casein. The peptide backbone has been replaced by a double yellow ribbon. Neutral side chains are colored cyan, hydrophobic side chains green, acidic side chains red, and basic side chains purple. sl




Color Plate 20. (Top) Energy minimized casein asymmetric submicelle structure, i.e., one ^-casein B, four a -casein Β and two /3-casein A asymmetric dimers. Ribboned backbones without side chains; ^-casein Β in cyan, a -casein Β in red and white; /3-casein A backbone colored in magenta. (Bottom) Energy minimized casein symmetric submicelle structure, i.e., one ^-casein, four a -casein Β and two /3-casein symmetric dimers. Ribboned backbones without side chains; ^-casein Β in cyan, a -casein Β in red and white /3-casein A in magenta. sl

2

2

sl

sl

2

sl



Color Plate 21. Spacefill model of 180 residues of gly-ala-Hpro template energy minimized built structure of the triple helix of tropocollagen. Each chain is colored individually (magenta, green, and red-orange), to easily visualize the super-helix surface motif.




Color Plate 22. The regions of oxidation state dependent conformational change observed in solution and crystal forms of cytochrome c are visualized using the coordinates of tuna ferrocytochrome c. The exposed heme edge faces the viewer. Side chain atoms are shown for the heme bound Cysl4, Cysl7, Hisl8 and Met80, and also for Asp50. Residues with significantly different backbone conformations between the two oxidation states are shown in space-filling representation and color coded as follows: dark blue: those observed in the solution structures for the horse cytochromes (32, 42, 47-49, 52, 69, 72, 80, 82, 86); orange: those observed in the crystal structures of the tuna cytochromes (26, 50); light blue: those observed in both solution and crystal structures (27, 28). The heme is also shown in space-filling representation (in red), while the unaltered residues are shown using a solid ribbon tracing.




Color Plate 23. The main build-up steps used in the BUILD strategy are shown for the antiparallel dimer structures: (a) Cys -Pro-Ala-Ala-Cys ; (b) Cys -ProIle-Glu-Cys-Phe ; (c) Thi^-Asn-Val-Asn-Cys-Pro-Ile-Glu-Cys-Phe ; (d) Thr Asn-Val-Asn-Cys-Pro-Ile-Glu-Cys-Phe-Met-Pro . The selected orientation shows the inter-chain disulfide bonds at the center of each figure. Hydrogens are not displayed. Residue numbers with primes belong to the second (symmetrical) chain. Ribbon traces have been added to illustrate the symmetry in the backbone conformation of the two chains. 7

n

12

7

12

3

14

Color Plate 24. Stereo diagram of the final 16 structures for the Thr3-Prol4 dimer segment in the same orientation as shown in Color Plate 23.


Molecular Modeling

Recommend Documents