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      Kinemage Supplement to Branden & Tooze, 2nd Ed. - Table of Contents
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      Chapter 1 file:  c01-Basics.kin

 (Kin 1)   Polypeptide fragment: rotatable phi, psi & chi angles (Fig. 1.2,1.6)
 (Kin 2)   Disulfide formation: Cys SH vs SS forms (Fig. 1.4)
 (Kin 3)   Amino acid structures & roles, shown in DHFR (Panel 1.1)
 (Kin 4)   Side-chain conformations of leucine (Fig. 1.8)
 (Kin 5)   2-iron metal site in ribonucleotide reductase (Fig. 1.9a)
 (Kin 6)   Exercise finding dihedral angles & Calpha handedness (Fig. 1.7,1.2)

      Chapter 2 file:  c02-Motifs.kin

 (Kin 1)   Alpha helix, end-on as helical wheel and in context (Fig. 2.4b)
 (Kin 2)   Calpha backbone of thioredoxin, with mixed beta sheet (Fig. 2.7a)
 (Kin 3)   H-bonding in the mixed beta sheet of thioredoxin (Fig. 2.7b)
 (Kin 4)   Hairpin loops in antiparallel beta structure: SGPA (Fig. 2.8)
 (Kin 5)   Ribonuclease - all-atom & mainchain-Hbond representations (Fig. 2.9)
 (Kin 6)   Ribonuclease - ribbon & Calpha-SS representations (Fig. 2.9)
 (Kin 7)   Calmodulin - motifs & Ca++ binding loops (Fig. 2.13c, 2.13b)
 (Kin 8)   Handedness of crossover connections in beta sheet (Fig. 2.17, 2.18)
 (Kin 9)   Beta-alpha-beta motif in lactate dehydrogenase (Fig. 2.17)
 (Kin 10)  Triose P isomerase as 4 beta-alpha-beta-alpha units (Fig. 2.20)
 (Kin 11)  Exercise identifying correct handedness of motifs

      Chapter 3 file:  c03-Alpha.kin
 
 (Kin 1)   The 4-helix bundle of Rop protein (Fig. 3.6,3.8)
 (Kin 2)   Myohemerythrin, up&down 4-helix bundle and Fe ligands (Fig. 3.7a)
 (Kin 3)   Human growth hormone, 4-helix bundle of unusual topology (Fig. 3.7b)
 (Kin 4)   Farnesyl transferase A chain, an alpha-alpha superhelix (Fig. 3.9)
 (Kin 5)   Leu-rich repeat variant, a helix-hairpin sequence repeat (Fig. 3.9)
 (Kin 6)   Myoglobin ribbons, with 8 helices around a heme group (Fig. 3.10)
 (Kin 7)   Helix-helix packing by ridges into grooves (Fig. 3.11,3.12b)

      Chapter 4 file:  c04-Al_Bet.kin

 (Kin 1)   Animation of the open, twisted alpha/beta fold (Fig. 4.1b,4.2b)
 (Kin 2)   4-sidechain layers in the a/b barrel of glycolate oxidase (Fig. 4.3)
 (Kin 3)   Pyruvate kinase, an enzyme with 3 quite different domains (Fig. 4.5)
 (Kin 4)   Bifunctional a/b-barrel enzyme PRA-isomerase,IGP-synthase (Fig. 4.7)
 (Kin 5)   Active site animation for the a/b barrel enzyme RuBisCo (Fig. 4.8)
 (Kin 6)   The a/b "horseshoe" fold of ribonuclease inhibitor (Fig. 4.10-4.12)
 (Kin 7)   Open, twisted a/b folds: flavodoxin vs adenyl kinase (Fig. 4.14a,b)
 (Kin 8)   Carboxypeptidase - open a/b fold and active site (Fig. 4.19,4.20)
 
      Chapter 5 file:  c05-Beta.kin

 (Kin 1)   Cu,Zn superoxide dismutase, an antiparallel beta barrel (Fig. 5.1)
 (Kin 2)   Retinol-binding protein, an up&down beta barrel (Fig. 5.2-5.4)
 (Kin 3)   Neuraminidase, a 6-fold beta-propeller (Fig. 5.6-5.9)
 (Kin 4)   Gamma crystallin - repeats & Greek key motifs (Fig. 5.10-5.15)
 (Kin 5)   Flu hemagglutinin subunit, chains HA1 & HA2 (Fig. 5.20)
 (Kin 6)   Flu hemagglutinin jellyroll Greek key beta barrel (Fig. 5.23)
 (Kin 7)   Animation of hi- vs low-pH forms of hemagglutinin (Fig. 5.25-5.27)
 (Kin 8)   Alkaline proteinase, a 2-sheet parallel beta-helix (Fig. 5.28)
 (Kin 9)   P22 tailspike protein, a 3-sheet parallel beta-helix (Fig. 5.29)
 (Kin 10)  An exercise in identifying protein folds

      Chapter 6 file:  c06-FldFlx.kin

 (Kin 1)   Barnase - Calphas and some folding-study mutants (Fig. 6.4)
 (Kin 2)   Disulfide-bond isomerase: domains, SS, & surface (Fig. 6.8)
 (Kin 3)   Animation of cis-trans peptide isomerization (Fig. 6.9)
 (Kin 4)   Cyclophilin (Pro isomerase), with cis Ala-Pro bound (Fig. 6.10)
 (Kin 5)   Animation of GroEL vs GroEL/GroES chaperonin complexes (Fig. 6.13)
 (Kin 6)   Conformational changes of domains in a GroEL subunit (Fig. 6.12a)
 (Kin 7)   Animation of conformational change in hexokinase, on sugar binding
 (Kin 8)   Conformational changes in CDK2 upon binding by cyclin (Fig. 6.17)
 (Kin 9)   Calmodulin - animation of motion on peptide binding (Fig. 6.21)
 (Kin 10)  Alpha-1 antitrypsin, intact vs cleaved forms (Fig. 6.23a,b,6.22)
 (Kin 11)  Allostery in phosphofructokinase (Fig. 6.25-6.27)
 (Kin 12/13)  Exercise in looking at protein motions - LDH, MBP

      Chapter 7 file:  c07-DNA.kin

 (Kin 1)   DNA base pairs (A-T, G-C), with Hbonds & atom balls (Fig. 7.4-7.7)
 (Kin 2)   B form DNA duplex, 12 base pairs  (Fig. 7.1,7,2a)
 (Kin 3)   A form DNA duplex, 8 base pairs  (Fig. 7.2b)
 (Kin 4)   Z form lefthanded DNA duplex, 10 base pairs  (Fig. 7.2c)
 (Kin 5)   Tyr tRNA, with the 4 stem-loops, modified bases, & tertiary Hbonds
 
      Chapter 8 file:  c08-HthTF.kin

 (Kin 1)   Lambda Cro, & 5 helix-turn-helix motifs superimposed (Fig. 8.3-8.5)
 (Kin 2)   Lambda repressor/DNA complex - overview of dimer (Fig. 8.6-8.9)
 (Kin 3)   Lambda repressor/DNA - details of interactions (Fig. 8.14-8.17)
 (Kin 4)   Animation of allosteric changes in Trp repressor (Fig. 8.18-8.20)
 (Kin 5)   Lac repressor tetramer - core & 4-helix domains (Fig. 8.21,8.22)
 (Kin 6)   PurR/guanine/DNA binding (Fig. 8.23)
 (Kin 7)   CAP protein dimer vs CAP/DNA, animation (Fig. 8.24)

      Chapter 9 file:  c09-EuTF.kin

 (Kin 1)   TATA-box binding protein/DNA complex (Fig. 9.4-9.7)
 (Kin 2)   Engrailed homeodomain/DNA complex: helix-turn-helix (Fig. 9.8-9.11)
 (Kin 3)   Mat alpha1 - Mat alpha2 DNA complex, ribbons (Fig. 9.12)
 (Kin 4)   Oligomerization domain of p53 tumor supressor (Fig. 9.17)
 (Kin 5)   DNA-binding domain of p53 tumor supressor (Fig. 9.18-9.21)
 (Kin 6)   NF-kappaB dimer/DNA complex 

      Chapter 10 file:  c10-TFfam.kin

 (Kin 1)   A CCHH Zn finger structure (Fig. 10.1)
 (Kin 2)   Zif/268: 3 tandem CCHH Zn fingers, DNA complex (Fig. 10.3-10.6)
 (Kin 3)   Glucocorticoid receptor DNA-binding domains (Fig. 10.8-10.11)
 (Kin 4)   The 4-Cys binuclear Zn of Gal4, in DNA complex (Fig. 10.13-10.15)
 (Kin 5)   Leucine zipper peptide dimer from GCN4 (Fig. 10.18)
 (Kin 6)   MyoD dimer/DNA complex (Fig. 10.24-10.27)
 (Kin 7)   Max dimer/DNA complex ribbons (Fig. 10.28-10.29)

      Chapter 11 file:  c11-SerPr.kin

 (Kin 1)   Chymotrypsin - 2 domains, 3 chains, and catalytic triad (Fig. 11.7)
 (Kin 2)   Trypsin/BPTI - overview & nonspecific binding (Fig. 11.9)
 (Kin 3)   Trypsin/BPTI - catalytic features & contact dots (Fig. 11.9, 11.12)
 (Kin 4)   Chymotrypsin, trypsin, & subtilisin superimposed (Fig. 11.7,11.13)
 (Kin 5)   Subtilisin  - alpha/beta structure, in ribbons (Fig. 11.13)
 (Kin 6)   Subtilisin active site & eglin inhibitor (Fig. 11.14)

      Chapter 12 file:  c12-Membr.kin

 (Kin 1)   Bacteriorhodopsin 7-helix bundle, with trans-retinal (Fig. 12.3)
 (Kin 2)   Porin subunit - beta-strand ribbons, colored by hairpins (Fig. 12.7)
 (Kin 3)   Porin trimer - Calphas, lipids, aromatics, pore charges (Fig. 12.8)
 (Kin 4)   K+ channel tetramer, with ion pore (Fig. 12.9-12.11)
 (Kin 5)   Photosynthetic reaction center, with pigments (Fig. 12.14-12.16)
 (Kin 6)   LH2 light-harvesting complex, 9-fold ring (Fig. 12.17-12.19)
 (Kin 7)   An exercise in viewing membrane proteins - cytochrome oxidase

      Chapter 13 file:  c13-SigTr.kin

 (Kin 1)   Ras p21 oncogene: binding of a GTP analogue (Fig. 13.4,13.5)
 (Kin 2)   G protein switch animation, in transducin alpha (Fig. 13.6-13.10)
 (Kin 3)   Transducin beta - 7-fold beta propellor (Fig. 13.13)
 (Kin 4)   Transducin beta - detail of WD repeat (Fig. 13.14)
 (Kin 5)   Transducin heterotrimer complex (Fig. 13.15)
 (Kin 6)   Complex of human growth hormone with its receptor  (Fig. 13.20)
 (Kin 7)   Hck Tyr kinase: SH3, SH2 & kinase domains (Fig. 13.30)
  
      Chapter 14 file:  c14-Fiber.kin

 (Kin 1)   Collagen triple helix (Fig. 14.1-14.4)
 (Kin 2)   An alpha-helical coiled-coil, from tropomyosin (Fig. 14.6b)
 (Kin 3)   Animation of myosin conformational change (Fig. 14.15, 14.16)

      Chapter 15 file:  c15-Immun.kin

 (Kin 1)   Immunoglobulin domains - CL, VL, light chain & FAB (Fig. 15.7-15.11)
 (Kin 2)   Intact IgG molecules, Y-shaped vs T-shaped (Fig. 15.17)
 (Kin 3)   Lysozyme/antibody complex - overview & spec. binding (Fig. 15.15-16)
 (Kin 4)   HLA-A2, an MHC class II antigen, with bound peptide (Fig. 15.18-20)
 (Kin 5)   T-cell receptor, complexed with MHC class I (Fig. 15.22-23)
 (Kin 6)   Multiple fibronectin domains (Fig. 15.24)
 (Kin 7)   Two domains of CD4, with beta ribbons (Fig. 15.25)

      Chapter 16 file:  c16-Virus.kin

 (Kin 1)   Icosahedron, dodecahedron, cube, and symmetry axes (16.2-16.3)
 (Kin 2)   T=1 viral symmetry, vs icosahedron and dodecahedron (16.4-16.5)
 (Kin 3)   STNV subunits: icosahedral T=1 symmetry and axes (16.5b, 16.14a)
 (Kin 4)   TBSV subunits A vs C, conformational difference animated (16.8a)
 (Kin 5)   TBSV: 3 subunits around the pseudo-3fold axis in a T=3 virus (16.9)
 (Kin 6)   Jellyroll Greek key fold of viral proteins, for STNV (16.13, 16.14a)
 (Kin 7)   MS2 capsid protein dimer, with bound RNA (16.17-16.20)
 (Kin 8)   SV40 virus - pentamer & subunit organization (16.23-16.26)

      Chapter 17 file:  c17-Engin.kin

 (Kin 1)   Canonical structures for immunoglobulin loop CDR H2 (Fig. 17.2)
 (Kin 2)   T4 lysozyme 1-, 2-, & 3-SS stabilizing mutants (Fig. 17.3)
 (Kin 3)   T4 lysozyme helix-charge, Gly->Ala, & Ala->Pro mutants (Fig. 17.5)
 (Kin 4)   Phage-selected EMP1 peptide/erythropoetin receptor (Fig. 17.11-12)

      Chapter 18 file:  c18-StDet.kin

 (Kin 1)   Crystal packing for scorpion toxin (like Fig. 18.3)
 (Kin 2)   Concanavalin A, colored by crystallographic B-factor
 (Kin 3)   CCHC Zn finger: multiple NMR models (like Fig. 18.20)