Kinemage Supplement to Branden & Tooze, 2nd Ed. - Table of Contents

		Contents of file c1Basics.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 in finding dihedral angles & Calpha handedness (Fig. 1.7,1.2)

		Contents of file c2Motifs.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}* - An exercise in identifying correct handedness of motifs

		Contents of file c3Alpha.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)

		Contents of file C4Al_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)
 
		Contents of file c5Beta.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 - repeated domains & 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

		Contents of file c6FldFlx.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}*, *{Kin 13}* An exercise in looking at protein motions - LDH, MBP

		Contents of file c7DNA.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
 
		Contents of file c8HthTF.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)

		Contents of file c9EuTF.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 

		Contents of file c10TFfam.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)

		Contents of file c11SerPr.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 - 4 essential features (Fig. 11.14)

		Contents of file c12Membr.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

		Contents of file C13SigTr.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)
  
		Contents of file c14Fiber.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)

		Contents of file c15Immun.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)

		Contents of file c16Virus.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)

		Contents of file c17Engin.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)

		Contents of file c18StDet.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)