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Home , Taliglucerase alfa

Index

AAA ATPases 55 aldolase-catalyzed reactions ABC chondroitin 74 asymmetric aldol reactions 291 acarbose 517–518 cell-based synthesis 275 2-acetamido-2-deoxy- -glucopyranose aldolases 740–741 DHAP-dependent 276–280, N-acetyl-chitobiose 617d 283–284, 289–291 N-acetyl kanosamine 607 engineering 277, 280 N-acetyl lactosamine 607, 610–611, synthetic applications 276–278, 283 619 aldopentoses 3, 5 N-acetyl-neuraminic acid 610 aldotetroses 3–4 N-acetylgucosamine 740–741 algasidase alfa 501 endo N-acetylglucosaminidase 626 algasidase beta 501 N-acetylhexosaminidases 745, 747, 541 -β-749 alkylation of monosaccharides 20 acid/baseβ- catalyst 220–221 -allose 3 aclacinomycin A 332, 334–335 allosyltransferase 651 acrylamide 35 alternand 786, 788 actinohivin 479 alternansucrases 639 active molecular species 104 -altrose 3 Alzheimer 60, 480–481, 491, 532, 540, ADAMs 74 d 545 ADAMTSactive site 74specific chaperone 527 Alzheimer’s disease 480–481, 491, adenocarcinomas 486 532, 540 adhesin 202 amphotericin B 92, 672–674 adhesion 148, 151, 156, 158, 161–162, amphotericin B glycosylation 673 175–177, 179–180, 184–185, 323 200–205 a-amylase 513–514, 517 adhesion-inhibition assay 203 aducanumab 540 amyloid monomers 482 amyloid precursorfibrils 477, protein 482 481 170, 172–173, 177–178, 181, affinity186–192, 149–150, 201, 155–157, 204 164, amyloidosis 482 African sleeping sickness 538 amylopectinamyloid-β-peptides 323–324 482, 540 aggrecan 67, 74 amylosucrases 641, 643 aggresome-like induced structures 59 androgen-sensitive human prostate agrin 469, 481 adeonocarcinoma cells 487 Agrobacterium 690 angiogenesis 473–475, 483, 488, 509 AIDS 89, 92, 99, 476, 493, 511, 548–549 243, 249 aldohexoses 3, 5 anomericretention configuration and inversion 218–221, of 243 240, 1012 Index

anomeric effect 9, 15, 22, 25 anomers 6 Bacillus anthracis tetrasaccharide 42 anthrose 42 Bacillusβ-hydroxydecanoic circulans AM7 acid 789 697, 699 antibiotics Bacillus circulans OKUMZ 31B 797 aminoglycoside 92–94, 96, 98 Bacillus circulans T-3040 794 Bacillus globisporus C11 786 resistance 78–79, 96–99, 101, 103 Bacillus globisporus secondβ-lactam generation 78, 92, 95, 101 98 Bacillus megaterium 649 anticoagulants 472–473 Bacillus stearothermophilus N75 790 792 Bacillus subtilis 686 antimicrobial photochemistry 104 antithrombin-bindingT-antigen Galβ1,3GalNAc motif 168 473 benznidazole 511 antithrombin III 67, 472, 541 benzoxazin-3(4basic fibroblast Hgrowth)-one factor33 475 antitrypsin null Hong Kong 53

a1-antitrypsin 532 antitumor vaccines 42 bioethanolBifidobacter 993–996, 777 999, 1003, 1007 bifidobacterium-promoting activity 778 -arabinose 3 bioinformatics 30 argonauteapplication protein fields 755, 483 759 biomassbiofilm 184degradation 871 arraysd 181 biomass substrates 994 Arthrobacter sp. H65-7 784–785 biopharmaceuticals 37–38, 43, 539, Arthrobacter sp. K-1 778 541–542 Arthrobacter sp. Q36 764, 766–767 Arthrobacter globiformis 784, 788 biosimilars 38, 539, 543 N-aryl-3-alkylidenepyrrolinones 504 biosurfactantbiorefinery 898 708–710, 715, 717, 720, ASGPR 155, 177–178, 186 724–725, 732 Ashwell receptor 155, 178, 188 biosustainable 727 asialoglycans 377 biosynthesis asialoglycoprotein receptor 484 E. coli A 84, 86 asialoglycoprotein receptor (ASGPR) GDP-fucose 661, 666–668, 670–671 155 globo-H 509–510 Aspergillus 810, 813, 815, 817, glycans 658–659, 669, 674–675, 677 819–820, 824, 827, 830, 833, glycosphingolipids 509 836–838, 840, 844, 856–857, glycosylphosphatidylinositol 860, 862 537–538 Aspergillus niger ATCC20611 773 proteoglycans 33 Aspergillus oryzae 780 staphyloxanthin 102 ATP11A 45 UDP-galactose (UDP-Gal) 661 Au nanoparticles 113 bis(monoacylglycero) (BMP) aurincarboxylic acid 504 504 autoinducer (AI) 705, 710 blood–brain barrier 535 avermectins 337 blood group antigens 147, 165 avilamycin A 333, 338 bovine serum albumin 489 branchedboronate affinityderivatives sandwich of cyclic assay 110 B cell homing 65 nigerosylnigerose 788 branching enzyme 792

β-hydroxyalkanoic acid 697, 703 Index 1013

breast cancer 60 catalytic nucleophile 248, 252–253 bundles 181 catalytic sites 748, 751–752 Burkholderia 700, 721, 724, 730 catalytic subsite 248 butirosin 95–97, 100 catechol 512–513 butirosin B 95–96 cathepsin 497–498 CAZy (Carbohydrate-Active ) 658, 810, 814–815, 820, 822, CACO-2 cells 518 824–825, 827–828, 830–831, calcitonin 38 833, 835–836, 838, 855 calcium absorption 778 CAZy database 910–911 calnexin 46, 49–50, 54, 518, 527, 544 Cbz-trileucine vinyl sulfone 60 calreticulin 46, 48, 518, 527, 544 cell adhesion molecules (CAMs) 151 Campylobacter sp. 354 cellobiohydrolase 899 Campylobacter jejuni 349, 391 cellobiose 10–11, 242–248, 257–258, cancer 30, 35, 38, 45, 60, 62, 65, 70, 260–262, 265–266 72, 107–108, 112, 114, 570–571, glycosidic bonding 10 573–574, 577, 581–582, 596–599 biomarkers 474, 487 745, 749, 812, 818, 822–823, stem cells 474, 509 α-cellobiosyl833, 852–854, fluoride 863, 628 868, 996– capsular polysaccharide 350 1000, 1002, 1004–1005, 1007 carbohydrate 1–2, 4, 6, 8, 10, 12, 14, 16, production costs 999 18, 20–22, 24, 26–28 cellulolytic enzymes carbohydrate binding modules 811, 813 heterologous expression 927–928, carbohydrate conformation 167, 173 930, 932, 934, 936, 938, 940, carbohydrate esterase 810 942, 944–954, 956, 958, 960, 962 carbohydrate–lectin complex 164–165, cellulose 323, 325, 328, 739, 742, 173, 175 744–745, 749, 758, 811–819, carbohydrate–lectin interactions 200 821–824, 827, 830–831, 833, carbohydrate–protein interactions 148, 836, 863–866, 869, 874, 887, 181, 185–203, 206 898–902, 908–913, 915–916, carbohydrate recognition domains 29, 918, 993–1000, 1002–1007 36, 48, 149 cellulose degradation 930, 937–939 cellulosic biomass 993–998, 1000, 169–170, 200 1002, 1004, 1006, 1008 carboncarbohydrate nanotubes specificity 32, 112–113 149–150, cellulosic fuels 965–966 Cardin and Weintraub motifs 470 cellulosome 913–915, 917–918 cariostatic activity 783 ceramide 491–493, 503, 509, 519, 521, catalytic acid/base 248 528 catalytic acid-base 248, 252 cerebroside 491 catalytic residue 768–769, 782 , Chagas disease 510, 513 8 CH-π bonding 174 6 chaperon-mediated therapy 519, 523 catalyticcatalytical mechanism core structures, 239, types:245–246, (β/α) chaperones 46–47 248,(α/α) 252–253,, α+β, -like 256 748 chemical 526 double displacement mechanism chelate effect 189–191 752 chemoenzymatic synthesis 297–315, single displacement mechanism 751 603 1014 Index

chitin 79–80, 82 colon cancer 475, 488 colon carcinoma 487, 518 chitin deacetylases 745, 754, 758 colorectal carcinomas 487 chitin-modifyingα-, β-, and γ-chitin organisms 740–741 744 combinatorial biocatalysis 309, 314 chitin oligosaccharide deacetylases 745 complexation via Ca 170 chitin oligosaccharide elicitor-binding concanavalin A 1132+ protein 82 concanavalin A (ConA) 150 chitin synthases 745 743–744, 748–749, 751, Cahn-Ingold-Prelog (CIP) rules 5 753–756, 759 configuration/ notation and 5nomenclature 4 chitooligosaccharide R-/S notation 5 deacetylase 80 Fischerd l projection 4, 10 sulfotransferase 80 conformation 7–9, 12 1 chitosan 741–742, 745–746, 755, C4 conformation 8 4 757–758 C1 conformation 8–9, 12 chondroitin sulfate 68 axial substituents 8 chromocyclomycin 331, 334 boat conformation 8 chromomycin A3 331–334 chair conformation 7–8 CI-7, CI-8, CI-9 793 equatorial substituents 8 clan 217 open chain form of sugars 6–7 conformational itinerary 246–247, 251 7, 9, 11, 13, 15 conformational space 197–198 classificationaldoses 2, of 16–19 carbohydrates 2–3, 5, congenital disorders of glycosylation ketoses 2, 16–19 468 oligosaccharides 12 consolidated bioprocessing 948–949 clathrin 177 Consortium of Functional Glycomics clearance of serum glycoproteins 178 30, 104 click chemistry 199 188–189 Clostridia 914, 917 negative 188 Clostridium acetobutylicum 906 positive 188–189 Clostridium cellulovorans 906, 914–915 core 1 synthase 63 Clostridium thermocellum 907, 913 core 3 synthase 65, 487 cluster 793 Cosmc molecular chaperone 488 clustering 177–179, 181, 186, 190 coupled metabolically engineered clusters 165, 173, 179 bacteria technology 660 CMP-N -neuraminic acid 299 coupling reaction 782, 795 Creutzfeldt–Jakob 467, 481, 532 CMP-sialic-acetyl-β- acid synthetased 571, 585 critical micelle concentration (CMC) CMP-sialicCMP-Neu5Ac acid 610, transporter 618 571, 580, 700 586 crude extract 719 coagulation factors 532 crystal structure 782 cohesin 935–937, 948 curdlan 664 cohesin–dockerin interactions 911, 914, 918 colitis 486–487, 539 cyclic β-1,2-glucan synthase 795–797 collectins 152, 155–156 cyclic maltosylmaltoseβ-1,2-glucans 795 786, 788–789 cyclic β-glucans 795 Index 1015

cyclic nigerosylnigerose 786–788, 790 DFA V 783–784 cyclic pentasaccharide containing 1-3, di-rhamnolipid 698, 706, 721 1-4, and 1-6 linkages 790 diabetes 513, 515, 517, 532, 539 cyclization reaction 794, 797 diabetes mellitus, type 2 515, 517 cycloamylose 791–792 difructose anhydride (DFA III) 783–784 cyclodextrin 790 dihydroxyacetone (DHA) 279, 281 dihydroxyacetone phosphate (DHAP) 612 generation 278 cycloinulohexaosecyclodextrin-α,1-4-glucosyltransferase 797–798 glycolytic pathway 283 cycloinulooligosaccharide fructotransferase 797 -glucopyranoside 627–628 cycloinulooligosaccharides 797 disaccharides2,4-dinitrophenyl 2, 10, 237–244,2-deoxy-2-fluoro- 246–248, cycloisomaltooligosaccharide (CI) 793 250,β-d 252, 254–266, 268, 270, 272 cycloisomaltooligosaccharide cellobiose 10 glucanotransferase (CITase) 793 cyclomaltodextrin glucanotransferase (CGTase) 782, 788–790, 794 lactoseα-1,4′-glycosidic 11 linkage 10 cystein proteases 57 β-1,4′-glycosidic linkage 10 sucrose 11–13, 19 cytokines 38, 61 tableα-maltose sugar 10 12 cystic fibrosis 47 disproportionation reaction 789, 795

dockerinsdisulfide 935, 937 486 DC-SIGN 36, 158–159 dolicholdisulfide reductase,45 ERdj5 54 DC-SIGN-related-glucopyranosyl molecule 159 phosphate double displacement-like mechanism DC-SIGNR613 159 248, 252, 255 2-deoxy α-d double displacement mechanism 511 deoxygalactonojirimycin 501–502, drug delivery 38, 112 2′-deoxy-lactose525 607 dTDP-2,6 deoxysugars 309 deoxyjirimycin -rhamnose 315 n-butyl~ 526 dTDP-deoxysugars 302–303, 315 n-nonyl~ 526 dTDP-GlcdTDP-β-l pyrophosphorylase 303, 313 deoxymannojirimycin 51 dTDP-nucleotidylyltransferases 303 1-deoxymannojirimycin (DMJ) 287 durhamycin 334

516, 518–519 deoxysugars1-deoxynojirimycin 34, 94 (DNJ) 287, 502, dermatan sulfate 68, 73 eleutherobin 32 dermatitis 493 Ebola Zaire virus strain 542 deubiquinating enzymes 57 Eliglustatassay) 522, 203 524 dextrandetoxification sulfate 32–33 479 endo-actingELISA (enzyme-linked 216, 219 immunosorbent dextransucrase 638, 641, 643 endocytosis 178, 183 DFA I 783–784 endogalactosylceramidase 493 DFA IV 783–784 endoglucanases 812, 814, 816, 863, 899 1016 Index

endoplasmatic reticulum 491, 527, -fagomine 287 537, 544 fatty acid de novo synthesis 701 Fibrobacterd succinogenes 906, 912 675 Fibrobacteres model 913, 918 endothelialendoplasmatic growth reticulum factor (ER) 72 44–45, endoxylanases 823, 825, 866 Enterococcus faecalis 690 fibroblast growth factor (FGF) 71 enthalpy 164, 189, 191 fibronectintype 1 175, 67, 184–185,72 202, 204 entropic gain 166 fimbriae entropy 164, 166, 189, 191 type 1 184 entropy loss 191 FimHfimbriae 175–176, adhesion 184–185 enzymatic biomass degradation 996 enzymatic synthesis 300, 303, 310, 314–315 flippase113 45–46 Fondaparinuxfluorescence resonance 472, 476 energy transfer foods for special health use (FOSHU) enzymed-enzyme engineering (4-α-glucanotransferase) 638–639, 643, 645791 763 enzyme efficiency 997 enzyme-inhibitor binding 998 formation of O- and N-glycosides enzyme replacement 498–499, 501, 524–525 1,2-cis glycosides 25 enzyme replacement therapy 38, 501, 1,2-α- andtrans β-glycosidation glycoside 25 22 524 direct anomeric O-alkylation 25 epigallocatechin-3-gallate 477 Koenigs–Knorr method 22 epimer 11, 19 formylglycine 507 Ca-formylglycine 507 Förster mechanism 113 EPO analogs52, 515, 41 526–528, 531 fructansucrases 643–645, 647, 649 ER-associated degradation 44, 47, 49, fructooligosaccharides 647, 775–778, erythromycinER-to-Golgi trafficking 95, 98 492 β-fructofuranosidase799 773, 776–779 ERAD-erythrose 44, 48, 3 50–54, 56–58 fructose 2–3, 7, 11–13, 17, 19 erythropoietin 542 fructose 6-phosphate aldolase (FSA) Escherichiad coli 184–185, 200–202, 281 349, 396 fucans 67, 81 recombinant 690 -fucokinase 306, 311 fucosyltransferase 609 exo-acting 216, 218–219, 229 fungil 810, 816, 818–819, 823, 825, 831, exoglucanasesuropathogenic 812–813, (UPEC) 815, 184 822 833, 835, 837, 846, 850, 852– exoglycosidases 495 853, 855–858, 860, 862–871 expansins 938 furanose 6, 22 extostosin-1 73 furanose conformation 773 furin 89, 478–479 extravasation 179–180 extracellular matrix (ECM) 31 gala series 492–493 Fabry 491, 496, 500–502, 519, 525, galacto(gluco)mannan 819, 834–835, 530, 532, 550 837–838, 868 Index 1017

galacto-N-biose 241, 262–263 glucansucrases 638–639, 647 galactokinase 301, 304, 310 40 galactooligosaccharides 779–781 glucomannans 327 -galactose 11, 13 galactose-1-phosphate phosphorylase (GH 94) d uridylyltransferase 304, 310 β-1,2-glucooligosaccharide796–797 galactosialidosis 497–498 glucosaminoglycans 478 α-glucopyranosyl- -glucose 6–7, fluoride10–11 627 β,1–3-galactosidase 617 - -glucose 6–10, 15, 22 galactosylβ,1–4-galactosidase ceramide 492 618, 620 α-glucosed 5–23 β-galactosidase 765,N-acetylhexosamine 779–782, 788 β -glucosed 608 phosphorylase 613 glucosed 1-phosphate 239–240, 243, β,1–3-galactosyl- l n-lactose 779 248–251, 254–262 galactosylsucrose 778 glucose dehydrogenase 777 galactosyltransferase(β-1,4-galactosyl) 605–608 glucosidase I 48 glucosidase II 48 galectin 152–153, 161–163, 179, a-glucosidase inhibitors 513, 517–518 β,1–4-galactosyltransferase182–183, 185 605 galectin-3 61 glucoside 21–23 β-glucosidase 899 maltooligosaccharide 790 galtamycinGalNAc kinase B 333,GK2 336 305 glucosyl-α-(1,4)-isomaltosyl-α-(1,4)- gangliosideGalNAc- mimics 367–368, 63 376 glucosylceramide 492–493, 502, 509, gangliosides 108, 491, 494–495 β-glycosylamine522–524 608 gangliosidoses 498–499 glucosylglycerol 242–243, 263–264 gastric carcinoma 487 6-O gastric glands 62 790 Gaucher’s disease 287, 502–503, glucuronidation-α-glucosyltransferase 35 786–788, 524–525, 542 glycan 29–30, 40–41, 43, 46, 48–49, GDP-activated fucose analogs 311 51, 53, 61, 63–66, 104–105, GDP-a- -mannose 299 107–110, 115–116 GDP-b- -Fuc pyrophosphorylase 311 glycan arrays 105 GDP-b-d-fucose 299, 304 N-glycan biosynthesis 183 Gerstmann–Strausslerl syndrome 481 glycans, high-mannose type 478–479 l -glyceraldehyde 3–4 GH 217–224, 228–229, 231–232 glyco code 206 GHGFP family fluorescent 240–252 tag 669 glyco-SAMd 106 GH family 13 768, 772, 789–790 glyco-SAMs 197, 199–200 GH family 32 777 glycoarray 203–206 Gibbs free energy 164 glycocalyx 147, 149, 175, 184–185, Gibbs–Helmholtz equation 164 202–205 O glycoclusters 193–198 Globo-H 509–510 glycocode 31 globotriaosylceramide-GlcNAc-cycling 35 493, 500–502 glycoconjugates 297, 299–300, globotriaosylsphingosine 502 303–304, 315, 467–468, 496, 511, 604, 621, 625, 637, 650

1,3-1,4-β-glucanase 628 1018 Index

glycodendrimers 193, 195–198 glycosyl acceptor 21, 24, 238 glycodendron 195 glycosyl donor 21–22, 258 glycosyl enzyme intermediate 247 glycoengineering 542 glycogenglycodiversification 239, 241, 253, 672–674 255, 258, 261 glycosyl 747, 749, 753 glycogen debranching enzyme 791 glycosyl hydrolasefluoride 227, families 229–232 747, 753 Glycogene Mutation Map 468 glycosyl transfer 237, 253, 265 glycogenin protein 34 glycosylation 322, 327, 329, 334–338 76, 79, 81, 83, 85, 87–89, cytoplasmatic 35 697 humanizing 43 glycolysis 701 secretory 33–35, 43–44 glycomics 29–30, 104–105, 108–109, 206 humanization 43 glycomimetics 148, 191–194, 196, 206 N-glycosylationprofile 44–45, 47, 49, 51, 53, glycoproteins 26–28 55, 57, 59 antifreeze 35 glycosylphosphatidylinositol 536 antiviral proteins (interferon) 27 glycosylsucrose 782–783 blood plasma proteins 27 glycosyltransferases 181–182, carbohydrate/carbohydrate- 237, 241, 243, 247, 299–300, recognition 27 302–306, 309, 313–315, 325, cell-surface glycoconjugates 27 327, 338, 357, 359–360, 362– collagen 27 363, 370–373, 376, 380, 382, follicle-stimulating hormones 27 385–386, 388–389, 658–659, HIV protease inhibitor drugs 27 663, 666, 672, 674–675 immunoglobulins 27 GT family 14 65 mucous secret proteins 27 superfamily GT-A 62 recombinant 37–38, 40, 42, 44 glycosynthase 228–229, 231–232, synthesis 41 257–258, 627–629 therapeutic 38, 42, 44 glypican 72 glycorandomization 100–101 glypican-1 481 glycosaminoglycan (GAG) analogs 355 GM1-gangliosidosis 496 glycosaminoglycans 31, 33, 67, 69, 71, GM2 activator protein 495, 498–499 73, 75 GM2-gangliosidosis 499–500 glycosidase 615–616, 618–619, 622, goblet cell 67 627, 629, 658, 675 Golgi apparatus 44, 62, 69, 88–89, 675 endo-glycosidase 625 Gram-negative bacteria 77, 83, 532 exo-glycosidase 614 Gram-positive bacteria 77, 533–534 glycoside 237–241, 243, 245, 247–248, 250, 255, 257–258, 266 GT family 241–242, 252–253 hydrolase 215–232, 240–241, GTgreen family fluorescent 84 797 protein (GFP) 204 245, 248, 813–814, 816, 835, -gulose 3 855–856, 858 (GT) 215, 217 d N-glycosides 21, 26 Haemophilus ducreyi 364 O-glycosylation 33, 39, 43, 44, 65, 105 Haemophilus influenza 349, 355, 364, glycosphingolipid microarrays 108 368, 377–378, 382 glycosphingolipids 467, 490–493, 495, Haworth projection 9–10 497, 499, 501, 503, 505, 507, 509 heat shock protein Hsp70 504, 508 Index 1019

Hehre resynthesis-hydrolysis 229–230 -idose 3 Helferich catalyst 23 IgA nephropathy 64, 497 Helicobacter pylori 349 immobilizedd cells 772 hemagglutinin 498 immobilized enzyme 776 hemicellulose 898–900, 909, 994–995, immunoglobulin (Ig)-like fold 159 1000 in situ product removal (ISPR) 720 heparan sulfate 68, 71–72, 110, 469, infection 176, 178, 202 471–473, 477–480 bacterial 201 473, 475, 482 MRSA 99 heparin 67–73, 75, 469–476, 478–481 urinary tract 202 heparin-binding growth factors 470 colonic 487 hepaticlow molecularasialoglycoprotein weight (LMW) receptor 472 inflammation 156, 176–177, 179, 202 (ASGPR) 155 hepatitis-C 36 inflammatory bowel disease 67, 486 heterologous expression 674–675 inflammatory response 179 70, 498–499 inhibitioninfliximab 539 hexoses 7 influenzaof glycosidases viruses 108–109 515 constant 997 highly branched cyclic dextrin 792 insulin Histophilushigh endothelial somnus venules 363 (HEVs) 66 HIV 36, 41, 92–93, 99, 476–480, 511, recombinant 38 519, 521, 544 integrinlactose-modified 67, 476 42 HIV-1 gp120 477–478 a interferon 39, 43 horseradish peroxidase 114 interleukins2β1 488 61, 66, 83 hOS-9homoserine lectin lactonedomain (HSL) 53 705, 710 intermolecular maltosyl transfer 789 hOS-9 mutant 53 internal return-like mechanism 253, human genome 658 256 humanized protein pharmaceuticals International Diabetes Federation 659 513 Hunter syndrome 69–70 hyaluronan 68. See also hyaluronic acid 790 hyaluronic acid intramolecular transferα-1,6-glycosyl reaction transfer 792 class I synthase 684 intramolecular transglycosylation 791 class II synthase 684 inulin 855–861 molecular weight control 693 inulin fructotransferase 784–785 synthesis pathway 687 inulinases 855–860 hydrogen bond networks 170 inverting GH 223, 229 hydrogen/deuterium exchange mass iso-neogala series 493 spectroscopy 530 isocyclomaltohexaose 790 hydrolysis 238–239, 243, 251, 254, isocyclomaltooligosaccharide 259, 812, 814, 816, 818–820, glucanotransferase 789–790 823, 826, 834, 840, 855–857, isocyclomaltopentaose 786, 789–790 859–862, 866 isofagomine 516, 523, 529 hydrophobic interactions 165, 174 isoglobotriaosylceramide 493 hyperthermophilic bacteria 941–942, isolation chip strategy 535–536 952 isomalto-oligosaccharides 640 1020 Index

isomaltose 641–642 legume 152–153, 167, 170 prebiotic 641 3-O 155 isomaltulose synthase 771–775 P-typemammalian 153 hepatic lectins (MHLs) ITAM-α-isomaltosyltransferase 161 786–788 S-type 161 iteratively 321–324, 326, 328–340, 342, 344, 346, 348 leukocytes 156–158, 172, 178–180 ITIM motif 161 Leloirleukocyte glycosyltransferase 177–179 605 levan fructotransferase 784 levansucrase 644, 646–647, 649, 779 kanamycin 93–94, 100 x trisaccharide 36 keratan sulfate 68, 75, 497 lignin 900–903, 909 kestose 649 lignocelluloseLewis 909, 913, 996, 1003 1-kestose 777 lipid A 83–87 keyhole limpet haemocyanin 489, 509 lipid A motif 84 Koenigs–Knorr method, mannoside 21 lipid A sensing methods 87 Krabbe disease 502, 505–506 lipid-rafts 490

lipooligosaccharides 670 lactacystin 60 lipopolysaccharideslipid-rafts (LRs) 490 31, 79, 81, 83, 85, lacto-N-biose 261, 263 87, 89, 350, 532 Lactococcus lactis 689–691 lipoteichoic acid 533–534 lactose 265, 820, 851, 862 living cell factory 665–666 lactosucrose 620, 765, 778–779 lyases lactosylceramide 492–493, 500 glycosaminoglycans 31, 33, 67 laminaribiose 242 lymphocyte homing 66 laminin 67 landomycin A 332, 335–336 lattices 153, 181, 183–184 LysM motifelicitor 82 receptor kinase 1 82 leaving group 247, 250 lysosomalLysM receptor-like degradation kinase 60 1/chitin lectin–carbohydrate lattice 162, 181 lysosomal storage diseases 37, 497, 523, 526, 544 lectin microarrays 107, 116 lysozyme 745–746, 748, 751, 753 lectin–sugarLectin Frontier complexes Database 166 30 lytic polysaccharide monooxygenases lectins 29–31, 36–37, 44, 48–49, 53, 61, 931, 938–939 77, 80, 105–108, 111, 115, 468, -lyxose 3 479, 490, 493–494 animal 150–152, 176 d array 105 macrolide antibiotics 92, 97 bacterial lectin FimH 175 Maillard reaction 35 C-type 36, 154–156, 158, 170–171 maltooligosyltrehalose 766–767, 770 maltooligosyltrehalose synthase 766, clustering 186 770 classification 149–150, 152 maltooligosyltrehalose trehalohydrolase endocytic 152, 155 766, 770 folddefinition 150–151, 148 153 maltose 242–246, 257–258, 261 I-type 159 mannanase 900, 916 Index 1021

microtubule dynamics 32 mannans 327 β-mannanase-mannose 3, 8355 mannose-6-phosphate receptor 151, MiglustatMiddle East 287, Respiratory 505, 522–524 Syndrome d 153 minicellulosomescoronavirus (MERS-CoV) 543 engineered 965–966, 968–988, (MMR) 155 990, 992 mannosemannose-specific trimming macrophage 49, 53–54 receptor minimal cocktail approach 1006–1007 minimal enzyme mixture approach mannosidase homology domain 51 1003, 1005 MBPβ-mannosidase C 156 835–836 miniscaffoldins 969, 971, 975–976, MCF7 cancer cells 489 982–983 melanoma lung metastases 475 mithramycin 331–332 mesenchymal stem cells 483 molecular diversity 203 metabolic carbohydrate engineering molecular dynamic (MD) simulations chitopentaose production 660 197 a-Gal epitope production 663 molecular mimic 352, 364, 367, 375, galactosides 662–665 378–379, 387 globotriose derivatives production molecular recognition 167, 174, 191, 663 202 globotriose production 662 mono-rhamnolipid 698–699, 706 lactose-derived oligosaccharides monoclonal antibodies 488, 539, 666 677 metabolic pathway engineering monosaccharides 683–684, 686, 688, 690–692, acylation of 20 694, 696 alkylation of 20 humanization of protein N-glycans montbretins A-C 514 674–675 Morquio, type B 497 molecular imaging 659, 668–669, Morquio, type A 497 671 MS fragmentation methods 488 oligosaccharide production 660, mucins 61–66, 110, 467, 483, 485–487, 662–663, 665 489 polysaccharide remodeling mucolipidoses 496 668–669, 671 mucopolysaccharides 68 metachromatic leukodystrophy 506 mucopolysaccharidoses 68, 496, 519 metachromic leukodistrophy 40 multienzyme routes 299 metagenome 908 multifunctional large protein 797 metastasis multiple myeloma (MM) plasma cells formation 473, 475 73 methicillin 98–99, 101 multiplexing 204–205 Mgat 181 multistep enzymatic synthesis 263 microalgae 39 multivalency 148, 153, 163, 173, 179, microarray technology 104 185–187, 189, 191, 193, 207 multivalency effects 148, 173, 179, 185, microorganisms 189, 191, 193 microfibrilsunculturable 740–741 536 multivalent 148–149, 163, 165, 185–193, 195–196, 202, 206 microRNAs 31, 483–484 1022 Index

multivalent glycoconjugates 193, nucleotide sugars 297–306, 308–310, 195–196 312–316, 318, 320 muraminyl sialylate 623 in situ (re)generation of 314 murein 742, 745–746 nucleotidylyltransferases 301, mutarotation 7 303–305, 307–310, 313–314 mutations germ-line 488 somatic 488 oleandomycin 98, 101 myelin-associated glycoprotein 623 oligosaccharides 2, 12, 22–23, 26, 239, myocarditis 511 261–262, 604, 609, 614, 619, 621, 623, 625–626 Bacillus macerans 12 -dependent catalysis 222 Bacillus megaterium 12 nanoparticles+ 69, 110, 112–113 chiral stationary phases 12 nanotechnologyNAD 30, 111, 113 cyclodextrin 12–13 nanotubes 32, 112–113 a-, b-, and g-cyclodextrin 12 cyclodextrin-glucanosyltransferase natural killer cells 476, 485, 494 12 Neisserianative chemical gonorrhoeae ligation 349, (NCL) 362, 40 364, linear 764 377 N-linked core 675 Neisseria meningitidis 349 plant 809–871 neogala series 493 oligosaccharyltransferase 46 neoglycoconjugates 493 olivosyltransferase 335–336 neoglycoproteins 41 omics technologies 691 neomycin 93–94, 97–99 omuralide 60 neurodegenerative diseases 467, 482, oncogenesis 469 491, 532, 540 oncomiRs 484 neutropenia 43 optical density (OD) readout 203 osmotolerant 795 type A 503 oxazoline 227–228, 232 Niemann–Picktype B 503 disease type C 287, 504 Erp57 48 p P. pastoris strain Nifurtimox617 511 humanized 675–676 p-nitrophenyl sialylateβ-galactopyranoside 623 palatinose 765, 771–773 nojirimycin 516, 521 pancreatitisPA-IIL 171 493 NMR spectroscopy 36, 111 PAO1 704–708, 728–729 non-natural amino acids 668 parasitic protozoa 538 non-naturalnon-Leloir glycosyltransferase sugar analogs 669 611 Parkinson’s disease 60, 491, 506 nucleophile 220–221, 223, 225, paroxysmal nocturnal hemoglobinuria 228–229, 231–232 538 nucleotide carba sugars 314 Pasteurella multocida 364–365, 368, nucleotide furanose sugars 312 373 nucleotide phosphono sugars 313 pathogen-associated molecular patterns nucleotide sugar donors 33 81 Index 1023

PC3 human prostate cancer cell line 487 potato phosphorylase 612–613 prion protein 467, 481, 537 pectate 901, 916 processive synthase 684 pectinpeanut agglutinin829, 831–832, (PNA) 839–841, 168 product inhibition 998, 1003 843, 845–852, 854, 868–869, promiscuity of enzymes 100 900–901, 915–916 prosaposin 496, 500 pectinases 852, 854 prostate cancer 486–487, 489 pectinolytic enzymes 839–841, 843, prostatic acid phosphatase 477 845, 847–849, 851–854, 868 Protaminobacter rubrum 771 protease, HIV-1 41 pentoses 7, 26 proteasomal degradation 47, 56–57 peptidoglycanPEGylation 42 31, 76–77 protective protein/cathepsin A 497 peptidoglycan glycosyltransferases 78 protein-carbohydrate interaction 168, perlecan 469, 481 173, 176 pharmacological chaperones 519, 526, 531 486 phosphacan 75 protein disulfide AGR2 phosphate 238–244, 246–262, 265 protein engineering 638 phosphate 244 protein structuredisulfide isomerases 367, 383 39, 47 phosphorolysis 238–240, 243, 246, proteins 249–252, 254–256, 258–261 BiP 54 phosphorylase 239–266 Photobacterium 364 extostosin 73 pili 175, 202 functionalEDEM 51–52 expression 38 fusion 676 plant cell wall degradation 918 glycan-binding 30, 105, 107, plantPL family polysaccharides 19 785 809–810, 822, 115–116, 468 851, 863 mannosidase-like 51 plasmid effect 693 penicillin-binding 78 plasmon resonance spectroscopy 106 scaffoldin 966, 969, 971, 982–983 polyhydroxyalkanoate (PHA) 701 sialic acid recognizing 569, 583 polymyxin 87, 92 activator 495 polysaccharide lyase 810 therapeutic 38, 40, 42, 44, 111 polysaccharides 2, 14, 21, 26, 322–323, tubulin 32 325–328, 340 Ub-like 57 amylopectin 14–15 ubiquitin-binding 57 amylose 14 proteoglycans 33, 67–69, 71, 73–75, a-glucosidase 15 110, 469–471, 477, 481 b-glucosidase 15 Pseudomonas 697–699, 701, 703–707, a 709, 711, 713–717, 719, 723, photoassimilation product 13 732, 735 starch-1,6′-glycosidic 12, 14 linkages 14 Pseudomonas aeruginosa 697, 701, 703, polyvalent 187–189 705, 707, 709, 711, 713, 715, Pompe disease 519, 531, 541 717, 719, 723, 732 posttranslational elongation 57 pseudomurein 77

46 psychosine 505–506 posttranslational modification 31, 34, PSGL-1 157–158, 172–173, 180 1024 Index

PTPz/RPTP 75 saccharide 1 pulmonary andβ activation regulated chemokine 503 Saccharomyces cerevisiae 689, 791 Purkinje cells 75 saccharificationrecombinant 898,918 902 pyranoses 6, 22, 25 saccharomycin 338 salinosporamide A 60 salvarsan 91 Q-bodies 59 Sandhoff disease 70, 499 quantum dots 111, 113 quorum sensing (QS) 703–704, 706 saponin QS-21A 489 saposinsSanfilippo 495–496,syndrome 500, 69–70 502–503, 505 saquayamycin Z 336–337 rapamycin-dependent scrapie 467, 481 hyperproliferation 486 SDR enzyme family 34 rate acceleration 238 reactions of carbohydrates 16–17, 19, secretase 481–482 21, 23, 25 secretorySEA domains trefoil 62 factors 62 aldonic acids 16, 18 selectin 61, 152, 155–158, 161, enolization 17 171–172, 179–180, 476 -glucitol 18–19 glycomimetic inhibitors 574, 581 -gluconic acid 16 d-mannitol 19 171–172 non-reducingd carbohydrates 17 E-selectin -selectin 42,65–66, 66, 156–157, 156–158, 167, 180, oxidationd of carbohydrates 16 476, 487 reducing carbohydrates 17 P-selectinl 156–158, 172, 180, 476 silver mirror test 17 sorbitol 19 66, 157, 180 Tollens reagent 16 self-assembledP-selectin glycoprotein monolayers ligand (SAMs) 1 (PSGL-1) 196 recognition processes 490, 494 semen-derived enhancer of viral recombinant therapeutics 539, 541 infections 477 renewable resources 725, 727 Serratia marcescens 744, 756 retaining GH 221–222, 228–229 shear-enhanced adhesion 202 rhamnolipid 698–703, 705–725, shear stress 202 727–731, 733 shigellosis 42 rhamnose 697, 701, 703, 706, 726 shotgun glycomics 108–109 rhamnosyltransferase 703, 705–706 sialic acid 33, 40, 42, 61, 65–66, 75 Rhizobium 764, 795, 803 analogs 670 -ribose 9 biosynthesis 571, 574, 585, 599, -ribose 3, 9 601 ricinβ-d 30, 88–89, 150, 152 sialidase d Vibrio cholerae 590

RING domain 58 sialidosis 496–498 rollingRNA-induced 179–180 silencing complex 483 sialoglycoconjugatesα-sialidase 621 622 RotavirusRNase C, retrosynthesis Haemagglutinin 41 (VP8*) x x) 157–158, 167, 592 171–172, 176, 180 Ruminococcus 907, 913–914 sialyl-Tnsialyl Lewis 487–490 (SLe Index 1025

sialyl-Tn antigen 661 Streptococci sialyl transferase group A 685 inhibitors 569–571, 574–582, 586, group C 685 589, 595 Streptococcus sp. 349 Streptococcus mutans 783 sialylation pathway 574 Streptococcus pyogenes 685, 373 sialylmimeticsα,2–3-sialyl transferase 585, 595 611, 618 Streptococcus zooepidemicus 687, 689, sialyltransferase 361–362, 365–369, 691–693 610–611, 618, 625 streptomycin 93–94 siglecs 61, 63, 152, 159–161 structural component 739–740, 742, sigma factor 706, 710 746, 756 signal transducer and activator of substrate-assisted catalysis 221, 232 transcription 3 474, 486 substrate engineering 637, 641–643, signaling molecules in symbiosis 795 647, 652 substrate/reaction engineering 280 SimpleCell 64 substrate reduction therapy 519, 524, singlesimian displacement-like immunodeficiency mechanism virus 479 544 249 sucrose 238–239, 241–243, 248–255, single nucleotide polymorphisms 468 257, 259–266, 639, 642, 644, single-walled carbon nanotubes 646–651, 855–861 112–113 sucrose analogue 649 sucrose isomerase 771 small–cell lung cancer 489 sucrose synthase 306, 315 solanezumabsiRNA 474, 485, 540 510 sugar 1–4, 9–10, 12–13, 16–19, 21, 25 solvation/desolvation energies 173 sugar code 206 solvent reorganization 166 sugar nucleotide recycle strategies 663 sortase-mediated transpeptidation sugar tree 3–4 968, 970 sulfatase source of metabolic energy 2 disease

265–266 lysosomal storage disorders 431, sphingolipidspecificity 247, degradation 250, 258–260, 70 cancer 436 and inflammation 431 sphingolipidoses 496 modulation of signaling 433 squalene synthase inhibitors 102 stability 259–260 type I mechanism catalyticmultiple aldehyde,sulfatase deficiency FGly 440 431 509 ping-pong 447 staphyloxanthinstage-specific embryonic 102 antigen 3 sulfatase localization, human starch 239, 253, 261, 273, 323–324, 764, 766–768, 770–771, 782– 451 783, 786, 788–789, 792–793, lysosomeextracellular 401, matrix 405, (ECM)431, 435, 431, 465 796, 799 secretory pathway 401, 406, 437 starch synthases 323–324 sulfatase structure residues 430, 444, 446, 589–590, 593–594 448–449 stemnessSTD NMR spectroscopy 474 581–586, catalytic domain 411, 421–422, streptococcal strain engineering 688 425–426, 433, 441–443 1026 Index

FGly 442 mucins 399–400, 403, 406, sulfatasepost-translational signature modification, sequence HNK 416–417, 403–404, 436, 419, 440 432, 451 441–442 sulfolipids 403, 406, 418 sulfatase substrates superbug technology 662–663 bacterial surfactant 700, 721 glycosaminoglycan degradation surfen 477 435, 439 Svennerholm abbreviations 491 mucin degradation 440, 462 Swainsonine 516 human swollenin 931, 938, 947 glycosaminoglycans 399, 406 syndecan-2 474, 481 heparan sulfate 404, 407, 409, syndecans 72–74, 474, 481 451 synthesis of glycosides 21–22, 24 sulfolipids 403, 406, 418 synthetic biology 43, 283, 291 unknown 405, 410–411, 437 systems biology 691, 693 systems biotechnology 728–730 sulfotransferase 402 sulfatesulfatase modification 405 of carbohydrates sulfated carbohydrates 404 T antigen 63 sulfation state 401 T. reesei cellulases 999, 1004–1005, Sulfolobus acidocaldarius 764, 767 1007 sulfotransferase mechanism T-synthase 63–64, 488 PAPS 400–401, 406, 420–421, 423, taliglucerase-alfa 542 425, 427, 430, 451 talosaminuronic acid 76 sequential mechanism 430 -talose 3 transition state 427–429 Tay-Sachs 491, 496, 498–499, 519, 526 sulfotransferase structure teichoicd acids 532 carbohydrate binding teixobactin 535 gate(ing) residues 425 tetanus toxoid 489–490 tetrahydrolipstatin 504 413, 424–425, 435 Thermus aquaticus 770, 791 co-factor substrate binding specificity 403, 410, thiol-ene method 106 PAPS, P-loop 422–423, 425 thiourea bridging 199 PAPS, PSB loop 422–423 -threose 3 sulfotransferase substrates thromboses 74 d bacterial 8-barrel) 782 Tn antigen 63–64, 487 unknown 405, 410–411, 437 TIM barrela 61, ((β/α)71, 83, 90 human Nod factor 420 Toll-like receptors 81, 83, 489, 533 glycosaminoglycans, ceratan toxinTNF- coregulated pilus 103 sulfate 415 toxins glycosaminoglycans, chondroitin/ cholerae 103 dermatan sulfate 404, 407, malarial toxin 1 42 413–414 Shiga 88–89, 495 glycosaminoglycans, heparan trans-sialidase 622 sulfate 404, 407, 409, 451 transaldolase B variants 281 glycosaminoglycans, keratan transfructosylation 778 sulfate 404, 407, 415–417 transgenic animals 541 Index 1027

transglycosylation 224–225, 227–229, UDP-a- -xylose 301, 312 232 UDP-b- -arabinose 301 trehalose 764–768, 770–771, 795, 799, ulvans d 81 803 unfoldedl protein response 52 a,a-trehalose 246, 252, 255, 260 unusual sugars 34, 94 trehalose-6-phosphate synthase/ trehalose-6-phosphate phosphatase 770 vaccines, cancer treatment 485 trehalose glycosyl transferring synthase valiolamine 518 770 vancomycin 92–94, 100–101, 329, trehalose phosphorylase/glucan 339 phosphorylase 770 vascular cell adhesion molecule-1 476 trehalose phosphorylase/maltose vascular endothelial growth factor 474, phosphorylase 770 488 trehalose synthase 770–771 vector-borne diseases 538 trehalulose 771–774 525 triantennary glycans 182 voglibose 517–518 Trichoderma 810, 813–814, 822, 828, von Willebrand factor 62 833 vorinostat 504–505 tumor angiogenesis 473–474, 483, 488 tumor-associated antigens 485 tumor microenvironment 483, 488 water problem 173 weak interactions 173 tyrosine gate 175–176 wheat germ agglutinin 36, 115 Tyr-tRNA 42 white rot fungi 909 whole exome sequencing 468 ubiquitin 47, 53–57, 59, 63 Wingless-related integration site 468 ubiquitin- 53 ubiquitination pathway 57 ubistatinsubiquitin-specific 60 protease 54 xenobiotics 35 UCH9 334 xylanX-omics 813, 728 819, 821, 823, 825–833, UDP-2-azido-2-deoxy- -galactose 311 836–837, 851, 866–867 xylan-binding module 972 305 d xylanase 900, 916 UDP-GalNAc pyrophosphorylase AGX1 xylans 325 UDP-glucose 797 xyloglucan 325–326, 811–817, UDP-glucoseUDP-GlcNAc glucosyltransferase 182–183 48 819–822, 824, 829–830, 833, UDP-N-acetyl-a- -galactosamine 299, 863, 865–866 304 xyloglycan galactosyltransferases 325 UDP-N-acetyl-a-d-glucosamine 299, -xylose 3, 607–608 304 UDP-nucleotidylyltransferasesd 301 d UDP-a- -galactose 299, 301, 304 β-xylosidases 823, 828–829 UDP-a- -glucose 299, 301–302 Yos9 (yeast osteosarcoma-9) protein UDP-a-d-glucuronic acid 299, 301 53 d d

Volume 2 Volume on Biocatalysis Biocatalysis on Pan Stanford Series Stanford Pan Peter Grunwald Peter edited by by edited Handbook of Carbohydrate-Modifying Biocatalysts

Handbook of Carbohydrate-Modifying Biocatalysts Grunwald V527 978-981-4669-78-8 Prof. Jon S. Thorson Jon S. Prof. ISBN Prof. Edward A. Bayer Edward Prof. .” Weizmann Institute of Science, Israel Institute of Science, Weizmann University of Wisconsin-Madison, USA Wisconsin-Madison, of University studied chemistry theatUniversity ofSaarbrücken andthe .” PeterGrunwald University of Hamburg, Germany, where he graduated in the field of high-frequency spectroscopy, and then became a staff member of the of Institute Physical Chemistry. After receiving his PhD the in Departmentphysical of chemistry Chemistryfrom at the a University biotechnologyof Hamburg, researchhe founded group. He was appointed professor in 2001. This book represents “This a book timely represents contribution to the field of carbohydrate-modifying enzymes. In many respects, understanding the chemistry and structural aspects of carbohydrates and their interactions is particularly challenging for students and established scientists alike. The many excellent chapters provide a comprehensive journey into the realm of carbohydrates, from the basics to up-to-date approaches and applications. I recommend this book to my own students and to all scientists interested in biological processes enzymes in gaining advanced knowledge of carbohydrate-modifying “This is an excellent compilation of the latest in research the field of biocatalysis carbohydrate-modifying and glycoscience With field. the in experts recognized highly by written biocatalysts emerging as fundamental contributors to a diverse array of scientific disciplines ranging from pharmaceutical development to renewable this energy, book is particularly timely and should for inspiring scientists and students serve as an excellent reference This book provides an actual carbohydrate-modifying overview biocatalysts. Carbohydrates of have the been structure, time disregarded by function, the for scientific community, and mainly a due application to long their complex of situation structure. Meanwhile, changed the with increasing knowledge about the biological key processes role carbohydrates such play as in recognition, others. An outcome of activitiesresearch in is glycoscience the development of several new signal transduction, immune responses, pharmaceuticals and against serious diseases such diseases. as malaria, Furthermore, cancer, and various theenzymes storage as well employment as microorganisms—will of of contribute environmentally significantly carbohydrate-modifying friendly to processes the developmentpetroleum- biocatalysts— boosting to bio-based production a of chemicals from renewable shift resources. of the chemical industry from The updated content of the second edition of this book has been extended by discussing the current state of the art biocatalysts of and using recombinantly the expressed synthesis carbohydrate-modifying bioprocessing of of lignocellulosic material. minicellulosomes Furthermore, a in synthetic asymmetric aldol reactions is presented. catalyze to aldolases using DAHP-dependent biology connection approach for with consolidated His research interests focus on the preparation and propertieskinetics of ofenzymes immobilizedin organic solvents,enzymes, and interactions between biocatalysts and heavy metal ions. Prof. Grunwald is also interested in chemical education, includingdevelopment. curriculum