Sacharidy a lipidy Glykobioinformatika a lipidoinformatika C2131 Úvod do bioinformatiky, jaro 2022 Lenka Malinovská Cukry 4.7.5 carbohydrate (saccharide) Monosaccharides, oligosaccharides and polysaccharides, as well as substances derived from monosaccha rides by reduction of the carbonyl group (alditols), by oxidation, including the oxidation of one or more terminal groups to carboxylic acids, or by replacement of one or more hydroxy groups by a hydrogen atom, an amino group, a thiol group, or by similar heteroatomic groups, This term also includes derivatives of these compounds, Note: The term carbohydrate was applied originally to monosaccharides, in recognition of the fact that their empirical composition can be expressed as CJHp)n. However, the term is now used generically in a wider sense. 4.7.35 monosaccharide Polyhydroxy aldehyde H-ICHOH^-CHO or polyhydroxy ketone H-[CH0H]n-CO-[CH0H]m-H, with at least three or more carbon atoms, respectively. Note 1: The generic term monosaccharide (as opposed to oligosaccharide or polysaccharide) denotes a single unit without glycosidic connection to other such units. Note 2: Most monosaccharides exist as cyclic hemiacetals or hemiketals. Examples: Aldoses, dialdoses, aldoketoses, ketoses, diketoses, as well as deoxy sugars and amino sugars, and their derivatives, provided that the compound has a (potential) carbonyl group. 4.7.37 oligosaccharide Compound in which monosaccharide units are joined by glycosidic linkages. Note: Oligosaccharides are called disaccharides, trisaccharides, tetrasaccharides, pentasaccharides, etc, according to their number of units, 4.7.38 polysaccharide Biomacramolecule consisting of a large number of monosaccharide (glycose) residues joined to each other by glycosidic linkages. See glycan Carbohydrate (saccharide) - cukr, sacharid - obecný termín pro celou skupinu látek Glykan - složitější cukr, oligosacharid nebo polysacharid, volný nebo vázaný V oboru chemie potravin jsou výrazem cukry označovány pouze monosacharidy a oligosacharidy. Dle legislativy jsou jako cukry označovány monosacharidy a disacharidy. V"^ n jměme ■ jzivové hodnoty B/100g 8/60g* %m 1 energetická hodnota Tuky ■ z toho nasycené Sacharidy ■ z toho cukr Bílkoviny Sůl 1485 kJ/ 352 kcal 6,4 g 1,9 g 59,1g 18.5i 9,2 g 10,0 g 0,08 g 1138 kJ/ 270 kca 5,8 g 2,2g 41,5 g 17,1 f 5,5 g 10,2g 0,20 g 14 8 II id 20 3 jfäň Priemerná — riikoň hodnota »/100g e/606« \R|] Energia 1485 kJ/ 352 kcal 6,4 g 1138 kJ/ 270 kcal POZOR! POUŽITI JEDNOTLIVÝCH TERMÍNŮ SE TEDY UŠÍ DLE VĚDNÍHO OBORU! Terminology of bioanalytical methods (IUPAC Recommendations 2018) https://doi.org/10.1515/pai 2016 1120 Received November 21, 2016; accepted February 1, 201S Cukry 4.7.5 carbohydrate (saccharide) Monosaccharides, oligosaccharides and polysaccharides, as well as substances derived from monosaccha rides by reduction of the carbonyl group (alditols), by oxidation, including the oxidation of one or more terminal groups to carboxylic acids, or by replacement of one or more hydroxy groups by a hydrogen atom, an amino group, a thiol group, or by similar heteroatomic groups, This term also includes derivatives of these compounds, Note: The term carbohydrate was applied originally to monosaccharides, in recognition of the fact that their empirical composition can be expressed as CJHp)n. However, the term is now used generically in a wider sense. 4.7.35 monosaccharide Polyhydroxy aldehyde rHCHOH^-CHO or polyhydroxy ketone H-[CH0H]rl-CO-[CH0H]m-H, with at least three or more carbon atoms, respectively. Note 1: The generic term monosaccharide (as opposed to oligosaccharide or polysaccharide) denotes a single unit without glycosidic connection to other such units. Note 2: Most monosaccharides exist as cyclic hemiacetals or hemiketals. Examples: Aldoses, dialdoses, aldoketoses, ketoses, diketoses, as well as deoxy sugars and amino sugars, and their derivatives, provided that the compound has a (potential) carbonyl group. 4.7.37 oligosaccharide Compound in which monosaccharide units are joined by glycosidic linkages. Note: Oligosaccharides are called disaccharides, trisaccharides, tetrasaccharides, pentasaccharides, etc, according to their number of units, 4.7.38 polysaccharide Biomacramolecule consisting of a large number of monosaccharide (glycose) residues joined to each other by glycosidic linkages. See glycan Carbohydrate (saccharide) - cukr, sacharid - obecný termín pro celou skupinu látek Glykan - složitější cukr, oligosacharid nebo polysacharid, volný nebo vázaný HLAVNI ŽIVIN • Bílkoviny • Lipidy (tuky) • Sacharidy - množstvím ve stravě (55-60% celkového energetického příjmu) představují její základní složku - poskytují organizmu energii ^ jiný biologicky význam je nepatrný^ www.vyzivaspol.cz Terminology of bioanalytical methods (IUPAC Recommendations 2018) https://doi.org/10.1515/pai 2016 1120 Received November 21, 2016; accepted February 1, 201S Funkce cukrů Funkce cukrů Výskyt cukrů v buňce Jádro - součást nukleových kyselin (ribosa, deoxyribosa) • Glykom - soubor všech sacharidů Cytosol - volné monosacharidy produkovaných organismem Endoplasmatické retikulum, Golgiho aparát - glykosylované proteiny (buňk°u>tkání) v daném čase za daných podmínek. Buněčná stěna - vázané oligo a polysacharidy Glykokalyx-glykoproteiny, glykolipidy ^^L^^^^^ Lipid Cukry *~UKry LUKryV 1 Protein Buňka ^ Výskyt cukrů v buňce • Kovalentně vázané cukry (monosacharidy, * Protože se nacházejí na povrchu buněk a oligosacharidy) se nacházejí na povrchu všech buněk. makromolekul, mohou se cukry uplatňovat v komunikaci a interakcích mezi buňkami a • Jsou součástí mnoha makromolekul. molekulami. • Mohou se v buňce nacházet i samostatně. Glykolipidy Glykoproteiny Cukry —^UKry LUKryV 1 Lipid Protein o3iY H'V'W ^1 Buňka ^ Výskyt cukrů v buňce Interakce buňka-buňka Interakce buňka-molekula Interakce buňka-patogen * Protože se nacházejí na povrchu buněk a makromolekul, mohou se cukry uplatňovat v komunikaci a interakcích mezi buňkami a molekulami. Patogen Molekula Buňka Buňka nformační potencia biomolekul Informační potenciál je určen množstvím „slov" (isomerů), které je možné sestavit z jednotlivých „písmen" (monomerů). Nukleotidy a aminokyseliny vytvářejí lineární polymery, spojované stále stejným způsobem (fosfodiesterová vazba, peptidová vazba). K dokonalému popisu obsažené informace stačí pouze jednoduchá sekvence (sled) monomerů: ATGCTGGTGATTGTGGATGCCGTTACCCTGCTGAGCGCCTATCCGGAAGCCAGCCGTGATC CGGCCGCCCCGACCGTGATTGATGGTCGCCACCTGTATGTTGTTAGCCCGGGCGATGCCGC MLVIVDAVTLL SAY PEASRDPAAP TVÍD GRHL Y WS PGDA Informační potenciál cukrů Pro přesný popis oligo(poly)sacharidu je kromě sekvence nutné znát i typ glykosidické vazby (anomerii) a velikost kruhu. D-glukosa + D-glukosa: al-2 al-3 al-4 al-6 al-1'a ßl-2 ßl-3 ßl-4 ßl-6 kojibiosa n ige rosa maltosa isomaltosa trehalosa sofo rosa laminaribiosa cellobiosa gentibiosa Informační potenciál cukrů Glykosidické vazby může tvořit i více nezjedná OH skupina, vzniká rozvětvený oligosacharid. Klasickým příkladem rozvětvených oligosacharidů jsou antigény ABO krevních skupin. Cukry mohou být dále modifikovány redukcí, oxidací nebo vazbou dalších funkčních skupin. o JcOOH^ NHAc Evolutionary aspects of ABO blood group in humans Massimo Franchini *, Carlo Bonfanti Department cf Hematology and Transfusion Medicine, Azienaa Ospedaiiaa Carte Poma, Mantova, Italy ABSTRACT The antigens of'the ABO blood group system (A, B and H determinants] are complex carbohydrate molecules expressed on red blood cells and oo a variety of other eel] lines and tissues. Crowing evidence is accumulating that ABO antigens, beyond their key role in transfusion medicine, may interplay with the pathogenesis of many human disorders, including infectious, cardiovascular and neoplastic diseases, hi this narrative review, after succinct description of the current knowledge on the association between ABO blood groups and the most severe diseases, we aim to elucidate the particularly intriguing issue of the possible role of ABO system in successful aging_ In particular, focus will be placed on studies evaluating the ABO phenotype in centenarians, the best human model of longevity. <£> 2015 Elsevier B.V. All rights reserved. Cukernv köd" w Kc Evolutionary aspects of ABO blood group in humans Massimo Franchirii *, Carlo Bonfanti Department cf Hematology and TrajisJusJort Medicine, Azienaa Qspedaliao Carte Porna, Maiitova, Italy ABSTRACT The antigens of'the ABO blood group system (A, B and H determinants] are complex carbohydrate molecules expressed on red blood cells and on a variety of other eel] lines and. tissues. Growing evidence is accumulating that ABO antigens, beyond their key role in transfusion medicine, may interplay with the pathogenesis of many human disorders, including infectious, cardiovascular and neoplastic diseases, hi this narrative review, after succinct description of the current knowledge on the association between ABO blood groups and the most severe diseases, we aim to elucidate the particularly intriguing issue of'the possible role of ABO system in successful aging_ In particular, focus will be placed on studies evaluating the ABO phenotype in centenarians, the best human model of longevity. <£> 2015 Elsevier B.V. All rights reserved. Cukernv köd" w Kc Krevní skupina 0 Tkáňové a krevní skupiny ABO CH2OH O 0<"wv Lipid GIcNAc Evolutionary aspects of ABO blood group in humans Massimo Franchini *, Carlo Bonfanti Department cf Hematology and Trajisjusjorr Medicine, Azienaa Qspedaliao Carte Porna, Maiitova, Italy ABSTRACT The antigens of the ABO blood group system (A, B and H determinants] are complex carbohydrate molecules expressed on red blood cells and on a variety of other cell lines and. tissues. Growing evidence is accumulating that ABO antigens, beyond their key role in transfusion medicine, may interplay with the pathogenesis of many human disorders, including infectious, cardiovascular and neoplastic diseases, hi this narrative review, after succinct description of the current knowledge on the association between ABO blood groups and the most severe diseases, we aim to elucidate the particularly intriguing issue of the possible role of ABO system in successful aging_ In particular, focus will be placed on studies evaluating the ABO phenotype in centenarians, the best human model of longevity. <£> 2015 Elsevier B.V. All rights reserved. Cukernv köd" w Kc OH CH2OH Gal CH2OH O Krevní skupina Tkáňové a krevní skupiny ABO Evolutionary aspects of ABO blood group in humans Massimo Franchini *, Carlo Bonfanti Department cf Hematology and TrajisJusJort Medicine, Azienaa Qspedaliao Carte Porna, Maiitova, Italy ABSTRACT Tlie antigens of the ABO blood group system (A, B and H determinants] are complex carbohydrate molecules expressed on red blood cells and on a variety of other eel] lines and. tissues. Growing evidence is accumulating that ABO antigens, beyond their key role in transfusion medicine, may interplay with the pathogenesis of many human disorders, including infectious, cardiovascular and neoplastic diseases, hi this narrative review, after succinct description of the current knowledge on the association between ABO blood groups and the most severe diseases, we aim to elucidate the particularly intriguing issue of the possible role of ABO system in successful aging_ In particular, focus will be placed on studies evaluating the ABO phenotype in centenarians, the best human model of longevity. <£> 2015 Elsevier B.V. All rights reserved. Cukernv köd" w Kc 0H CH2OH GalNAc LA^O OHcHoOH Gal HO- CH2OH O NAcI O Krevní skupina A Tkáňové a krevní skupiny ABO v Lectins Ctení „cukerného kódu" — Protilátky Lektiny - proteiny, které specificky a reverzibilně vážou mono- a oligosacharidy. Nejsou produkty imunitní odpovědi. Lektiny plní rozpoznávacia adhezivnífunkci v mnoha různých biologických procesech. Vyskytují se v zástupcích všech taxonů (rostliny, zvířata, houby, bakterie, viry). Hemaglutinin viru chřipky Virus chřipky A obsahuje povrchový glykoprotein, hemaglutinin (HA). Tento protein je lektin, který rozpoznává hostitelské buňky a řídí adhezi a vstup viru do buněk. New insights into influenza A specificity: an evolution of paradigms Ye Ji, Yohanna JB White, Jodi A Hadden1, Oliver C Grant and Robert J Woods Lektin Glykoproteiny a glykolipidy Hemaglutinin viru chřipky Virus chřipky A obsahuje povrchový glykoprotein, hemaglutinin (HA). Tento protein je lektin, který rozpoznává hostitelské buňky a řídí adhezi a vstup viru do buněk. New insights into influenza A specificity: an evolution of paradigms Ye Ji, Yohanna JB White, Jodi A Hadden1, Oliver C Grant and Robert J Woods Lektin Glykoproteiny a glykolipidy Ricin Ricin je toxin produkovaný rostlinou Ricinus communis (skočec obecný, Ricin obyčajný). Často využíván jako okrasná rostlina. Ricin se vyskytuje nejvíce v semenech. Pro otrávení jsou celá semena nevhodná, je nutné je pořádně rozžvýkat. Ribosome-inactivating proteins (RIPs) - proteiny inaktivující ribosomy Ricin, abrin, volkensin Adheze Glykoproteiny a glykolipidy Toxicita Buňka Ricin Tajné služby zadržely otrávený dopis pro Obamu. Obsahoval jed ricin 17. dubna 2013 18:06, aktualizováno 21:07 f) Q Q Americké tajné služby zajistily v úterý dopis adresovaný prezidentu Baráčku Obamovi, který obsahoval podezřelou látku. Dopis byl zachycen v objektu, který leží mimo komplex Bílého domu. Podle prvních testů federální policie obsahoval jedovatý ricin. Americkému senátorovi poslali dopis s ricinem Dopis zaslaný republikánskému senátorovi za stát Mississippi Rogeru Wickerovi obsahoval ricin. Potvrdil to předběžný test. jsou ale ještě potřeba další zkoumání. List se podařilo zachytit ještě v oddělení, které pro zákonodárce poštu zpracovává. O nálezu informoval šéf policie v Capitolu Kim Dine s tím. že případ převzal Federální úřad pro vyšetřování (FBI). Newyorskému starostovi poslali dopis s ricinem Dopisy adresované newyorskému starostovi Michaelu Bloombergovi a organizaci podporující omezení prodeje zbraní, obsahovaly jedovatí' ricin, uvedly úřady po testech. Jeden z bezpečnostních pracovníků, který přišel s dopisem do styku, vykazuje drobné příznaky kontaktu s ricinem. CBJštníko^>/ražda bulharského s p i s o va t e I e(Mar kova) ^-------**/oro jméno je neustále 7.9.2008 s námi... Londýn - Do dějin případ vstoupil jako „deštníková vražda" a dodnes není objasněn. Neznámý pachatel vpravil 7. září 1973 v Londýně pomocí speciálně upraveného deštníku jed do těla bulharského spisovatele a disidenta Georgiho Markova, který za čtyři dny zemřel. Podezření padlo na bulharskou komunistickou tajnou službu a kdysi obávanou sovětskou tajnou policii KGB. Podle některých spekulacísi zabití Markova, kterýv Londýně pracoval v bulharské sekci rozhlasové stanice BBC, objednal osobně vůdce bulharských komunistů Todor Žívkov, protože Markov, kdysi prominentní spisovatel a později ostrý kritik poměrů v Bulharsku, toho příliš mnoho věděl o životě bulharských vládců. Zajímavostí je, že 2ivkov slavil právě 7. září 1978 sedmašedesátiny. https://ct24.ceskatelevize.cz/archiv/1442570-destnikova-vrazda-bulharskeho-spisovatele-markova Glykoproteiny a glykolipidy Buňka Ricin není jed, ale projímadlo. Zemanovy výroky vyvolaly kritiku 3 6. května 2020 1S23 ^jfo^f Prezident Miloš Zeman vyvolal značnou kritiku mezi politiky, když v úterý popřel přítomnost ruského agenta v Praze a zkritizoval dvě zpravodajské služby. Řadu lidí popudil i tím, že ricin označil za projímadlo. Tajní Agent s ricinem pobouřil diplomacii. Radikální kroky nejsou třeba, říká Babiš © 28 dubna 2020 15:51, aktualizováno 20:51 Rusko popřelo informace týdeníku Respekt, že do Prahy dorazil agent tamních tajných služeb s jedem ricinem, kterého bezpečnostní úřady vyhodnotily jako riziko pro politiky Ondřeje Koláře a Zdeňka Hřiba. Rusko zprávu časopisu označilo za novinářskou „kachnu", to však česká diplomacie považuje za snahu o narušování svobody tisku. Senát žádá vládu, aby ohledně chování Ruska zakročila, podle premiéra Babiše ale nejsou potřeba radikální kroky. Newvorskómu starostovi |x>s|j|i il« •l>is s rk'iiH*m „Snad jeden z nejznámějších léčebných použití ricinového oleje je jako přírodní projímadlo. Je klasifikován jako stimulační projímadlo, což znamená, že zvyšuje pohyb svalů, které vytlačují materiál skrz střeva, a pomáhá tak vyčistit střeva. Stimulační laxativa působí rychle a běžně se užívají ke zmírnění dočasné zácpy." To si pan prezident plete s ricinovým olejem. Ricinový olej se vyrábí z těch stejných semen R. communis, která obsahují ricin. Ricinu se ale do olejové fáze moc nechce a olej je navíc ohříván, takže ricin (protein) je bezpečně denaturován. Ricin by pochopitelně skutečně fungoval jako projímadlo...taky je to emetikum a snižuje krevní tlak. Někdy až na nulu. Glykoproteiny a glykolipidy Buňka 88 Chem Soc Rev RSC Publishing Published OnlineFirst January 29, 2016; DOI: 10.1158/1535-7163.MCT-15-0633 REVIEW ARTICLE View Article Online Large Molecule Therapeutics Multivalent glycoconjugates as anti-pathogenic agents! Anna Bernardi.3 Jesus Jimenez Barbero,b Alessandro Casnati.c Cristina De Castrů,d Tamis Darbre* Franck Fleschi* Jukka Finne,9 Horst Funken.h Karl-Erich Jaeger,h Martina Lahmann,'Thisbe K. Lindhorst,-1 Marco Marradi,1 Paul Messner,' Antonio Molinaro,d Paul V. Murphy.1" Cristina Nativi,n Stefan Oscarso-n.0 Sdedad Penades.1 Francesco Peri.p Roland J. Pieters.q Olivier Renaudet/ Jean Louis Reymond* Barbara Richichi,n Javier Rojo.' Francesco 5ansone,c Christina 5 chaffer,1 W. Bruce Turnbull/Trinidad VelascoTorrijos,u Sebastien V id a I ,v Stephane Vincent.'"* Tom Wennekes* Han Zu i I hof1* a nd Anne Irnberty^ Molecular Cancer Therapeutics Gastric Adenocarcinomas Express the Glycosphingolipid Gb3/CD77: Targeting of Gastric Cancer Cells with Shiga Toxin B-Subunit Philipp Emanuel Geyer1, Matthias Maak1, Ulrich Nitsche', Markus Perl', Alexander Novotny1, Julia Slotta-Huspenina2. Estelle Dransart3-4 5, Anne Holtorf', Ludger Johannes34-5, and Klaus-Peter Janssen1 „DRUG-TARGETING" Jak jsou glykoproteiny kódovány v genomu? Glykom - soubor všech sacharidů produkovaných organismem (buňkou, tkání) v daném čase za daných podmínek. Glykosylace buněk - závisí na typu buněk, (zdravotním) stavu buněk, věku, prostředí. Glykosylace buněk (povrchové sacharidy) -využívá se pro komunikaci, interakce, specifické rozpoznávání mezi buňkami, popřípadě mezi buňkami a molekulami. Glykan Protein o- ATGTTGGTACGCTGACT GCCGTACGTAGCTTCGT GAC GT C GAT C GTAGCT G Gen Jak jsou glykoproteiny kódovány v genomu Enzymy = glykosyltransferasy, syntéza aktivovaných cukrů Nutná účast transportních proteinů! Struktura glykanů je v genomu kódována nepřímo Protein ATGTTGGTACGCTGACT GCCGTACGTAGCTTCGT GAC GT C GAT C GTAGCT G Glykosylace CDG (congenital disorders of glycosylation) - dědičné poruchy glykosylace. Glykosylace proteinů je složitý proces (syntéza aktivovaných cukrů, glykosyltransferasy, modifikace glykanů, glykosidasy), různých poruch glykosylace jsou tedy desítky. Tabulka f.- symptomy popisované u pacientů se syndromem CDG \a VJaobacni variabilní dysmoifie, invertované marnily, atypická distribuce tuku zejména v ojuteál-n í a ani lárni oblasti, poruchy rovnováhy, průjem, zvracen [. trom boembolie Chováni ŕasto extrovertní chováni, stereotypie Nervový syslím psychomotorická retardace (IQ 4D-Ů0), hypotonie, porucha sluchu, epilepsie, atrofie mozečku, poruchy myelinizace.riernoragické mozkové příhody, n europatie, snížená rychlost vedeni periferním nervem Odi stiabizmus, retinitis pigmentóza. katarakta Srdu peikardiálnľvýpotek, kardiomyopatie. vrozené srdeční vady Jitra hepatomegalie. hepatopatie Lad vlny proteinu rie, nefiotický syndrom Skelet kyfoskolióza. deformity hrudníku, kontraktjry Endokrinologie hypogonadizmus, ctiybejícl puberta, hypoglykemie Koagula» poruchy sráí livosti. krvácení, ale i embol ie, sníženi antitrombin ulil. faktom XI, protei-nuC. proteinu 5 Essentials of Glycobiology Essentials of Glycobiology, 2nd edition Chapter 42 Genetic Disorders of Glycosylation Kazuistika dívky s dědičnou poruchou glykosylace MUDr, Martin Magner, Ing. Kateřina Veselá, RNDr. Hana Hansi ková, CSc, prof. MUDr. Jiří Zeman, DrSc, MUDr. Tomáš Honzík, Ph.D. Klinika dětského a dorostového lékařství, 1. LF UK a VFN Praha Disorder Gene Enzyme OMIM Key features o- tr.r-.tiple p3.th"V3.v iäfects CDG-Ia PMM2 phosphomarir_ori"mtat e II 212065 mental re:"rĽa7.:or. (MR. : hypotonia, esotropia, lipodystrophy CDG-Ib MP1 p ho sp ho m amio s e 602:57? CDG-Ik ALG1 ami csy .transferase I GDP-Man: GlcNAc2- PP- CDG-Ic CDG-Id ALG6 ALG3 zlueosvltransrlerase I: Dol-P-Glc: Maii(,GlcNAc2-PP-Dť. iluí-;-;y.!:ii::i:"ť-:'aií Dol-P-Man: 60314: 601 LÍC CDG-IL ALG9 Do! ľtiumoivl- transferase mannosyltransíerase Dol-P-Miti: Mang and MansGlcNAc2-PP-Dol :"i ?.i in o "y It r ans íerase ManjGlcNAc2-PP-Dol tnaiiiiosy ltran s f era s e CDG-Ea MGAT2 G k 1\ Ac-trati "í era s e I (GnT II) CDG-Ie DPMI Dol-P-Man synthase I 60350: CDG-If MP DUI GDP Man: Dol-P-matinosy ltran e f era s e r.cr.cata.yt.c pictem 60879í CDG-IIb CDG-Ilc GLS1 SLC35C1ÍFUCT1 a 1-2 srncosiolase I GDP-fucose- transport e: Dol-P-Man Dol-P-Glc addition CDG-Hd BAGALT 1 51-4 galaczcs.v transferase CDG-Ig ÄLG12 Dol-P-Man: Man7GlcNAc2PP-Dol mannosy ltran s fera s e 60714: CDG-He COG! iciiärr.'sd o Isomeric G:lzi cotr.clsx šubu".it CDG-Ili ALGS zlucosvltransíera-e IE Dol-P-Glc: GlcjManoGlcNAcj-PP-Dol ilu;c-;yLtra:"s:?:"a" i 60S 10i CDG-Ľf COGK deficiency SLC3SA1 COGS CľvIP-sialic acid transporter ľiietr.bíi of tlie COĽ- CDG-Ii ALG2 minnojyltraiiíieraie II GDP-Man: 60790t ccmplex :bľ Golsi traífickitíř ManiGlcNAc2-PP-Dol mannosy Ltran s f era s e COG1 deficiency COG1 metnaei c: tlie COG ■: c tuple x fc-ľ Gclsrr 608540 severe psychomotor retardation, hypotonia, acquired m;-:rc:epli_.v. ior.\ CTa'cle -evct-ieí. :'evet, ;c a:?r.l:-ca:ky: neplnene svndiotr.e, earlv death 60S í severe v.ucrccephaly, r_ypotcni3.: seizures, liepate megaly 111066 VIR, cystr.c-rcr.inr.. sterectyv.eje.zuie* dysmorphism, r_v::e:ctna. liep.v: ~tr.ez3.lv. hepatic :"V-c-" Is death at 25 months) 606056 2 6c 2re:uirent infections-, p;:sister.- r_ei.vtrevr_i2a, \'3.: tr._:toceplialy h>iioionia (normal Tt) '1 -0 1 r.v-ooTC-r.ia iir."'j-.,rhv■. :::?j:ec-ui r.e:riciir.3.;e. D.~.r.;lv-Walter malformation 60S779 fatal ::i ;a:\v :lti r-\ c111intra; t?.bl= seizures, heparcrr.rzr.ly piogtess.:~.ejaundice, recurrent infections, cardiac failure :?'.■:imnment ■.ji. líiv-lih. |itci:-.-i;. pc of an individua L The cpiijoictic infnrmation (OKA mrthylatoft pattrm and hiitcnr rode) ti es.pceií.1 ľy ™iikrablc ta enviionnunuJ efféet; in the early intrauteiinr and nm-natal drvclopment and many cenumn I ehvojeci d tieůiei ttkc i «51 a.b eady tt lhůt Time The cvidmees. itmwirig the link hetween epigeneties and g ryocaylation are sec umu latiny. Rcccnt piojrrcsi in high-thmugi put ífyconies, ^Jiomiei and cpi^cneji.-j--ji:\ i i-..i:ine i:i nedes of protebi Elyeosyla.di>n K verv euniplei A.eoordin3to the ccntml dogmacfniolceular biolog, fiineton ■. .ijh.-I. | ■■ -. uii. i - .Ljuiiiiii.j.: Ir. i k -in.-.n.ie. ^ kiel: i-.:etli:i: by the nueleotde sc^ucjKe in the eorrtipondin£ gene. Kowcvci, in the esjc of ^fyean moietici cf gtyeoproteijts, thrjr arr ievoal addili.'.ii.il Li;, ji- .-.i::iljv.ity hetwícn ;enea and tne finál jfyeůii itrudun:. The finál itníitují of each glyean ii tharfcír not cnccdcd di ncelly in thr gmúmr Blood Groups „j Red Cíli Antigens ABO genotype in the offspring ABO alleles inherited from the mother A AB A ABO alleles inherited from the father B AB B B A B O Dědičnost krevních skupin ohch,oh gal o H antigen deficiency is known as the "Bombay phenotype" (h hr also known as Oh) and is found in L of 10=000 individuals in India and 1 in a million people in Europe. There is no ill effect with being H deficient but if a blood transfusion is ever needed, people with this blood type can receive blood only from other donors who are also H deficient. (A transfusion of "normal" group 0 blood can trigger a severe transfusion reaction.) ch2oh o Bombajský fenotyp. Jedinci nejsou schopni vytvářet ani základní H antigén (defektní fukosyltransferasa). Vytvářejí se protilátky anti A, anti B i anti 0. Působí problémy při transfuzích a testech paternity. Vhodné jako zápletka do seriálů. http://www.ncbi.nlm.nih.gov/books/NBK2261/ Blood Groups mi Red Cíli Antigens Dědičnost krevních skupin In the show "General Hospital", the father of Monica's child was in doubt. Monica had blood type A (genotype AO) and her child had blood type 0 [genotype 00). Because the child must inherit an 0 allele from the father, the father could have the genotype AO, BO, or 00. In other words, the child's father could have blood group A or B or 0, which rules out Monica's husband Alan [type AB) and implicates Rick (type 0). Predicted ABO Genotypes Alan Monica Rick -0"-r-0 AB AO AO or BO AO or BO http://www.ncbi.nlm.nih.gov/books/NBK2261/ Monika má krevní skupinu A. Alan má krevní skupinu AB. Dítě má 0. Podvedla Monika Alana s Rickem??? Blood Groups mi Red Cíli Antigens Dědičnost krevních skupin However, Alan is the father! This is possible because both he and Monica are carriers of incomplete H deficiency (H/h}_ Their h/h child is unable to produce any ABO blood group antigens and so despite inheriting the A or B allele from Alan, the child's RBC"s lack the A and B antigens as in blood type 0. Actual ABO and Hh Genotypes Alan Monica Rick -O □ AB Hh AO Hh AO or BO, HH hh http://www.ncbi.nlm.nih.gov/books/NBK2261/ Alan je tatínek! Ale možná je příbuzný s Monikou (vzhledem k vzácnosti alely h)...To by byl vhodný námět pro další díl... „Because both parents must carry this recessive allele to transmit this blood type to their children, the condition mainly occurs in small closed-off communities where there is a good chance of both parents of a child either being of Bombay type, or being heterozygous for the h allele and so carryingJheBombay characteristic as recessive. Other examples may include noble families, which ar^nbreague to custom rather than local genetic variety." Cukry - zkratky a symboly Základní jednotky složitějších sacharidů jsou monosacharidy. NA/proteiny - základní jednotky (nukleotidy, aminokyseliny) jsou jasně definovány a jejich počet není velký. Monosacharidů je mnoho, proto u glykanů nelze (jednoduše) použít jednopísmenný kód. Problém: vazby, větvení, modifikace Vyvinuto a používáno mnoho způsobů, jak sacharidy znázornit. Na rozdíl od NA/proteinů se u cukrů velmi často využívá grafické znázornění Cukry - zkratky a symboly UNION OF PURE AND APPLIED CHEMISTRY https://www.qmul.ac.uk/sbcs/iupac/2carb/ ß-D-Galp- (l-*4-)- ß-D-GlcpN Ac - (l-»2)-a-D-Maiip (1-3 T 1 ct-L-Fucp Gal(p 1 -4-)Glc NAc- (p 1 -2)Man(a 1 - Fuc(ol1-3) GalCp 1 -4)[Fuc(od -3)]GlcNAc(ß 1 -2)Man(al ■ Tři IUPAC způsoby jak pomocí zkratek znázornit oligosacharid. IUPAC {a-D-Galf>NAc-(l ^3)-[a-l^Fucp-(l->2)]-p-D-Galp-(L->4)-p-D- GlcpNAc-Cl-^3)-p-D-Gal^(l->4)-p-D-Glcp} LINUCS [][b-D-Glcp] j [<4+l)][b-D-Galp] {[(3+l)][b-D-GlcpNAc]{[<4+l)][b-D- Galp] {[(2+1 )][a-L-Fucp] {} [(3+1 )][a-D-GalpNAc] {}}}}} LinearCode ANa3 (Fa2) Ab4 GNb3 Ab4 Gb4 (spaces added for clarity) GLVCAM OLN (OfA) ZLB 4Gn 3LB '1GB (with LinearCc-rJe precedence rules for branching) CFG Oxfurtl GLYCAM/ Oxford \a2 4 LN L—GN ■G <$> D~Gdp O o L D-Gal/?NAc □ ♦ LN D-Ghp • □ G D-Glc/fNAc ■ ■ GN L-ru3)-[a-L~Fucp-(l->2)]-p-D-Galp-(L->4)-p-D- GlcpNAc-Cl-^3)-p-D-Gal^(l->4)-p-D-Glcp} LINUCS [][b-D-Glcp] {[(4+l)][b-D-Galp] {[(3+l)][b-D-GlcpNAc]{[(4+l)][b-D- Galp] {[(2+1 )][a-L-Fucp] {} [(3+1 )][a-D-GalpNAc] {}}}}) LlnearCode ANa3 (Fa2) Ab4 GNb3 Ab4 Gb4 (spaces added for clarity) GLVCAM CFG Oxford GLYCAM/ Oxford OLN (Of A) ZLB 4Gn 3LB 4GB (with LinearCode precedence rules for branching) \a2 4 LN L—GN ■G D-Gal/ř O O L D-GalpNAc □ ♦ LN D-GIc/í D-Glc/fNAc ■ ■ GN L-Fucp A ❖ ť Oxford-tyf e linkags: ..... ot-linkage — P-linkage 2 Cukry - zkratky a symboly Standardizace symbolů: Symbol Nomenclature for Glycans (SNFG) https://www.ncbi.nlm.nih.gov/glycans/snfg.html Významná část glykobioinformatických nástrojů je zaměřená na grafické znázornění cukrů. Symbol Nomenclature for Glycans (SNFG) Standardization in drawing glycan structures is essential for efficient communication. The tools and methodology illustrated here have become widely accepted by the scientific community. Use of these symbols to represent monosaccharides is now strongly recommended for all manuscripts submitted to major journals and other publications. Citation: • Symbol Nomenclature for Graphical Representation of Glycans, Glycobiology 25: 1323-1324, 2015. Citation link (^(PMID 26543186). • Updates to the Symbol Nomenclature for Glycans guidelines, Glycobiology 29:620-624, 2019. Citation linkte (PMID 31184695). EXAMPLE FROM YEAST Man nan s from 5. cerevisiae (P=phosphoiylJ EXAMPLES FROM SLIME MOLD Blood group antigens: H antigen on Type-1 lactosamine chain R=glycan backbone 3fP A antigen B antigen O-linked glycans (GalNAc type) Extended core-1 glycan %er/Thr 6'sulfo-sialyl Lewis-X on core-2 glycan ♦£lcr %er/Thr Cukry - zobrazovací nástroje rOj^DrawGlycan-SN FG \ i htt p *//\a/\a/\a/vi rt u a I g lyco m e org/DrawGlycan/ IU PAC-condensed Input ŕglycan or glycopeptide): Mar(a2]Man[a6)[Man[a2]Man{a3)]Man{a6)Gal(a3]Fuc{a6)Man(:a2)Man[aS) [Man[a2)Man(a3)]Man{a6)Gal(a3] Basic options: Display Linkage: Linkage font size: 16 Text font size: 16 Symbol Size: | Medium t | Orientation: | Left Other options (show/hide) Mass Option: None Adduct: None Molecular Weight: 2254.7562 Glykosylace • Glykosylace je významná posttranslační modifikace. • Ovlivňuje strukturu proteinů, jejich aktivitu i funkci (rozpustnost, stabilita, interakce, význam pro imunitní systém). • Glykosylace probíhá u eukaryot i prokaryot. A Repository of Experimentally Characterized Glycoproteins and Protein Glycosyltransferases of Prokaryotes ProGlycProt Second Release ProGlycProt is a manually curated. comprehensive repository of experimentally characterized glycoproteins and glycosyltransferases that are involved in protein glycosylation, in bacteria and archaea, exclusively. The website is a focused effort to provide concise and relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, attached glycans, linkages, their glycosylating enzymefs], their specificities, mutants, glycosylation linked genes, and genomic context thereof, in a cross-referenced, interactive manner... More»> ProGPID PraG P470 (Putative u n di ara rterized prateinJ Validation Status Characterized Organism Information Organism Name Bi.rkl-ckle'a cenacepac'a K5Č-2 Domain Bacteria tlassifi cation Family: Burkholderiaceae Order: Burkholderiales Class: Betaproteobacteria Division or phylum: "Proteobacteria" Taxonomie ID (NCBI) 985075 Protein Information Protein Name Putative uncharacterized protein LhiProtKB/SwissProtlD B4EB72 NCBI RefSeq WPJWH868B7.1. EM BL CDS CAR53291.1. UniProtKB Sequence !-tr|B4EB72|B4EB72_BURCJ Putative exported protein OS=Burkholderia cenocepacia (strain ATCC BAA-245 IDSM 16553 / LMG 16656 / NCTC 13227 /J2315 / CF5610) GN=BCAL2973 PE=+ SV=1 MKS LVQAV WAAALVA PWS FAQS GSTIT RAQVRAE LVQ LQQAGYNSA RGEDPHYPEAIQ AATARIAEQQRSALAQAQGADVSGYGAQAQGASASGSRAMGVRPASAEEMKSLVRGS Sequence length 117 AA Subcellular Location Outer membrane Glycosylation Status Glycosylation Type 0- (Ser/Thr) linked Experimentally Validated Glycosite(s) in Full Length Protein S106 Glycosite(s) Annotated Protein Sequence itr|B4EB72|B4EB72_BURCJ Putative exported protein OS=Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF561Q) GN=BCAL2973 PE^t SV=1 MKS LVQAV WAAALVA PWS FAQS GSTIT RAQVRAE LVQ LQQAGYNSA RGEDPHYPEAIQ AATAR1AEQQ RSALAQAQGA DVSGYGAQAQGASASGS RA M GVRPAs- (10S)A E E M KS LYRG S Sequence Around Glycosites [21 AA) GSRAM G VR PASA E E M KS LYRG Technique(s) used for Glycosylation Detection ZIC-HILICJmmunoblottingjtryptic digestion, and MS/MS analysis Technique(s) used for Glycosylated Residue^) Detection MS/MS analysis Glycan Information Glycan Annotation Tnsaccharide HexNAc-HexNAc-Hex. BCSDBID 1205 S GlyTouCan G71937MV PrSGlycProt http://www.proglycprot.org/ Protein Glycosylation in Prokaryotes Glykosylace TRĚfilDSin Microbiology Vůl. 11 No.l2 December 20tí • Glykosylace je významná posttranslační modifikace. • Ovlivňuje strukturu proteinů, jejich aktivitu i funkci (rozpustnost, stabilita, interakce, význam pro imunitní systém). • Glykosylace probíhá u eukaryot i prokaryot. A Repository of Experimentally Characterized Glycoproteins and Protein Glycosyltransferases of Prokaryotes ProGlycProt Second Release ProGlycProt is a manually curated. comprehensive repository of experimentally characterized glycoproteins and glycosyltransferases that are involved in protein glycosylation, in bacteria and archaea, exclusively. The website is a focused effort to provide concise and relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, attached glycans, linkages, their glycosylating enzyme{s], their specificities, mutants, glycosylation linked genes, and genomic context thereof, in a cross-referenced, interactive manner... More»> Sweet new world: glycoproteins in bacterial pathogens M. Alexander Schmidt1, Lee W. Riley2 and Inga Benz1 11nstitut für InfektioIogls, Zentrum far Molekularbiologie der Entzündung [ZMEE), Von-Esmarch-Str. 56, D-43149 Münster, Germany ^Division of Infectious Diseases and Immunity. School of Public Health, University of California, 140 Warren Hall, Berkeley, CA 94720, USA In eukaryotes, the combinatorial potential of carbohydrates is used for the modulation of protein function. However, despite the wealth of cell wall and surface-associated carbohydrates and glyco conjugates, the accepted dogma has been that prokaryotes are not able to glycosylate proteins. This has now changed and protein glycosylation in prokaryotes is an accepted fact I intriguing ly, in tiram-negative bacteria most glycoproteins are associated with virulence factors of medically significant pathogens. Also, important steps in pathogenesis have been linked to the glycan substitution of surface proteins, indicating that the glycosylation of bacterial proteins might serve specific functions in infection and pathogenesis and interfere with inflammatory immune responses. Therefore, the carbohydrate modifications and glycosylation pathways of bacterial proteins will become new targets for therapeutic and prophylactic measures. Here we discuss recent findings on the structure, genetics and function of glycoproteins of medically important bacteria and potential applications of bacterial glycosylation systems for the generation of novel glycoconjugates, PrSGIycProt http://www.proglycprot.org/ Protein Glycosylation in Prokaryotes Predikce glykosylace • Glykosylace je významná posttranslační modifikace. • Ovlivňuje strukturu proteinů, jejich aktivitu i funkci (rozpustnost, stabilita, interakce, význam pro imunitní systém). • Glykosylace probíhá u eukaryot i prokaryot. NetOGIyc -4.0 O-GalNAc (mucin type) glycosylate sites in mammalian proteins The NetOglyc server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. NetCGIyc-1.0 C-mannosylation sites in mammalian proteins The NetCGIyc 1.0 produces neural network predictions of C-mannosylation sites in mammalian proteins. DictyOGIyc-1.1 0-(alpha)-GlcNAc glycosylation sites (trained on Dictyostelium discoideum proteins) The DictyOGIyc server produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins NetNGIyc -1.0 N-linked glycosylation sites in human proteins The NetNglyc server predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence contextx£sn-Xaa-Ser/Thr^ sequons MINI REVIEW https://services.healthtech.dtu.dk/ Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds Predikce glykosylace • Predikce glykosylace: A/-glykosylace x O-glykosylace HO' HO- (a) --OH J^^O NH[ H ] CO NH3 COCH2—CH I coo- (b) COO" A/-glykosylace aminoskupiny asparaginu O-glykosylace hydroxylové skupiny serinu nebo threoninu Glycoproteins Tony Merry, University of Manchester, Manchester, UK Sviatlana AstraUtSOVa, Grodno State Medical University, Grodno, Belarus Based in part on the previous vers ion of this Encydo pedia of Life Sciences (ELS) article, "Glycoproteins"by "Jerry D Butters". Glykosylace chrání proteiny před proteolýzou, ovlivňuje strukturu a interakce proteinů, uplatňuje se v interakcích imunitního systému. Predikce glykosylace • Predikce glykosylace: A/-glykosylace x O-glykosylace HO' HO- (a) --OH J^^O NH[ H ] CO CH-, NH3 COCH2—CH I coo- (b) COO" A/-glykosylace aminoskupiny asparaginu Asn-X-Ser(Thr), X nesmí být Pro Asn-X-C- nekanonický motiv Záleží i na sousedních aminokyselinách, charakteru aminokyseliny „X" konformaci místa. O-glykosylace hydroxylové skupiny serinu nebo threoninu Nemají jasně definovaný motiv Identification of novel N-glycosylation sites at non-canonical protein consensus motifs Mark S. Lowe n thai . Kiersta S. Davis Trina Formolo Lisa E. Ki I pat rick, and Karen W. Phinney Analýza glykanů Charakterizace glykanů: hmotnostní spektroskopie (MS), vysokoúčinná kapalinová chromatografie (HPLC), nukleární magnetická rezonance (NMR). Biological sample Velká část softwarových nastrojuje zaměřena na zpracování a interpretaci experimentálních dat, analýza glykanů je bez využití bioinformatiky velmi obtížná (prakticky nemožná)... Separation'Enrichment Intact Glycoproteins Glycopcptidc enrichment after protease digestion Intaet tilvcopeptides Doglycosylation MS analysis WET-LAB DRY-LAB 2-OEgel LC/MS Multi LC 2-DE image analysis LC/MS image analysis WET-LAB MS and/or MS/MS MS/MS DRY-LAB Search database Identification 8c Update characterisation annotation Q I Database "Ü Bi. Degly cosy lated peptides 3 io informatics analysis 1 MS analvsis Released ulycans S MSai alysis Protein / Peptide identification Glycan structure identification and attachment site assignment Separation Bioinformatics Mass Spectrometry Bioinformatics Feng Li1-2, Olga V. Glinskii'-3 and Vladislav V. Glinsky'-2 Proteorrtics 2013, 13.3*1-354 DOMa.1t)02/pmic.201200149 Resouoe Pcxtól GlycoMod Home i Contact https://web.expasy.org/glycomod/ gariExPASy KüHj Qtii'• Bioirrformaiics Reamrce Portal GlycoMod Tool GlycoMod Home i Contact GlycoMod is a tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses The program can be used for free or derivatized oligosaccharides and for glycopeptides [Documentation / Mass values / Reference I Disclaimer] Note: You can use GlycanMass to calculate the mass of an oligosaccharide structure from its oligosaccharide composition Enter a list of experimental masses: 1041 72 ieS3,S3 1333,73 - 1131 62 1111.77 1142.97 ■ 1153 CI 1157 .91 1192.8.8 1238 23 1274.33 1286.18 1356 47 1371.45 1386.38 - 1418 45 1430.57 1435.42 All mass values are * average or O monoisotopic. Or upload a file, containing one mass per line, from your computer: Vybrat soubor Soubor nevybrán Mass tolerance: +/- 0.2 Dsltori >pdbI1TKAI A Chain A, 1 Transketolase QFTDIDKLAVSTIRILAVDTVSKANSGHPGAPLGMAPAAHVLWSQMRMNPTNPDWINRDREVLSNGHAVA LLYSMLHLTGYDLSIEDLKQFRQLGSRTPGHPEFELPGVEVTTGPLGQGISNAVGMAMAQANLAATYNKP GFTLSDNYTYVFLGDGCLQEGISSEASSLAGHLKLGNLIAIYDDNKITIDGATSISFDEDVAKRYEAYGW EVLYVENGNEDLAGIAKAIAQAKLSKDKPTLIKMTTTIGYGSLHAGSHSVHGAPLKADDVKQLKSKFGFN PDKSFWPQEVYDHYQKTILKPGVEANNKWNKLFSEYQKKFPELGAELARRLSGQLPANWESKLPTYTAK DSAVATRKLSETVLEDVYNQLPELIGGSADLTPSNLTRWKEALDFQPPSSGSGNYSGRYIRYGIREHAMG AIMNGISAFGANYKPYGGTFLNFVSYAAGAVRL SALSGHPVIWVATHDSIGVGEDGPTHQPIETLAHFRS LPNIQVWRPADGNEVSAAYKNSLESKHTPSIIALSRQNLPQLEGSSIESASKGGYVLQDVANPDIILVAT GSEVSLSVEAAKTLAAKNIKARWSLPDFFTFDKQPLEYRLSVLPDNVPIMSVEVLATTCWGKYAHQSFG IDRFGASGKAPEVFKFFGFTPEGVAEPAQKTIAFYKGDKLISPLKKAF 1041.72 1080.03 1093 73 1101.62 1111 77 1142 07 1153.01 1157.91 1192 88 1230.23 1274 33 1286 18 1356.47 1371.45 1386 38 1418.45 1430 67 1485 42 1531.45 1608.79 1628 84 1653.89 1670 17 1688 12 1708.08 1740.03 1766 29 1790.98 1869 04 1899 45 1960.28 2028.53 2047 74 2056.13 2105 32 2184 15 2201.95 2261.71 2316 35 2388.56 2429 00 2446 39 2457.63 2473.35 2545 02 2553.75 2604 07 2623 41 2702.62 2718.76 2761 27 2779.97 2805 59 2851 70 2867.83 2944.29 2975 04 3016.44 3028 57 3045 25 3113.17 3221.73 3245 86 3268.72 3345 42 3373 80 3535.19 3852.99 3868 36 3945.84 Peptides containi position -MC peptide mass [M] ling thd^rtiTN-X-S/T/C (X notPy^ peptide modifications 93-174 0 7900 79848 TPGHPEFELPGVEVTTGPLG QGISNAVGMAMAQANLAATY NKPGFTLSDMYTYVFLGDGC LQEGISSEA3SLAGHLK 359-388 0 3245 53768 LSETVLEDVYNQLPELIGGS ADLTPSNLTR 391-408 0 1863 93403 EALDFQPPSSGSGNYSGR User mass: 2761.27 Adduct ([M+H]+): 1.00727 glycoform ^mass structure type peptid,e,n peptide sequence glycopeptide mod. Links mass ualtori " mass [Ml _ mass (Hex)-, (NeuAc), 892.281 0 148 (NeuGc), - 1867 334 j^rToPPSSGSGNYSGR 2761 122 (Pent), 892.317 0.112 |^Ac)2 1867834 EALDFQPPSSGSGNYSGR 2761 158 GlyConnect 2 structures found in 1 peptide. Cukry - 3D struktura Co nás zajímá - struktury glykoproteinů, struktury sacharidů v komplexu s proteiny (lektiny, enzymy, protilátky). RTG krystalografie. Problém: velká flexibilita sacharidů (ve struktuře je viditelná jen část glykanu). Problém: Kvalita 3D struktur sacharidů v PDB může být nízká... Určení struktury komplexních sacharidů je obecně problém. NMR - tradiční metoda pro určení struktury oligosacharidů (práce v roztoku), problémy s přiřazením signálů a vyhodnocením dat (malé rozdíly mezi jednotlivými jádry). Molekulové modelování sacharidů je často nezbytnou součástí interpretace experimentálních dat. Cukry - 3D struktura Please select the desired monosaccharides and glycosidic linkages. If you are not sure how to do please look at the example page. An gvflmpii; fnr rnnrhri ntmrtimt nrr hrri ^Jemember - not all constructions are reasonably Input for the web-interface: A-D-MANP' 1-4' A-D-MANP' 1-4' A-D-MANP ' 1-4' A-D-MANP ' 1-4' A-D-MANP' 1-4' A-D-MANP ' SEND http://www.glycosciences.de/modeling/sweet2/doc/index.php It should be noted that under physiological conditions oligosaccharides are f re quejjtj^ highly loyiblo, and si ajgje static structure is an incomplete model. For this reason, the user is encouraged to employC^o^cular dynamics simulation^ develop a more complete understanding of the spatial and dynamic propertied ul" llitiir iiyiiluii.---- All builders at GLYCAM-Web generate molecular structure files that can be used in visualization programs or as input for simulations. For the builders that generate 3D structures from a primary sequence (e.g., DManpbl-eDGIcpNAcbl-OH), we offer the interfaces listed below for setting the primary sequence. GiyCAMt^ http://glycam.org/ Glykobioinformatika - databáze Databáze obsahující informace o proteinech (sacharidy jsou součást glykoproteinů, lektiny). Vlastní databáze sacharidů (struktury). Databáze enzymů a drah účastnících se syntéz a odbourávání glykanů (sacharidů). Informace o interakcích protein-sacharid „Glykocentra" - sdružené databáze, vlastní specializované databáze, analytické nástroje „Glykocentra" http://glyco3dxermav.cnrsir/home.php Disac3-DB GAG-DB GLYC03D 2.0 Glyko struktury BioOligo-DB Polysac3-DB NMR oligo CBMcarb-DB U ní lectin O Monosac-DB EPS-DB mAbscarb-DB Polys-Glycan Builder Other tools „Glykocentra" Cermav UNIVERSITĚ DE GENĚVE Unified exploration platform for manually curated and predicted lectins Unil_ectin3D Curated and classified lectin 3D structures PropLec Predicted p-propeller lectins LectomeXplore Predicted lectins in all available species from all kingdoms MycoLec Predicted lectins in fungal genomes TrefLec Predicted p-frefoil lectins ALGEA BUILDER BACTERIA BUILDER GAG BUILDER N-0 LINKED BUILDER PLANT BUILDER Glyco3D is a portal of databases covering the three-dimensional features of monosaccharides, di saccharides, oligosaccharides (Conformations and NMR spectra), polysaccharides, glycosyltransfe rases, lectins, monoclonal antibodies against carbohydrates, and glycosaminoglycan-binding proteins. These databases have been developed with non-proprietary software and they are opened freely to the scientific community. Each individual database stands by itself as it covers a particular field of structural glycosciences. http://glyco3d.cermav.cnrsir/home.php Glyco3D LYSAG?DB Identifikace a izolace nových lektinů gatagcgtaatgatcggctggctgccgcatttcatgctggtttcccaacgaaaat; tacäggtggtcgcgcccgccgccagcacatcgctgcgccaataatgatctttcägi ggtggcggcatcacgcacttccagttcgatcggggcaacaatgccggcatctttc: agcgcggtttcgcgcagatgcagctgatcacccgggctcagaccggtaaacagacl catacaggtggcgaccatcaatcacggtcggggcggccggatcacggctggcttci Genomy edrpikfstegatsqsykqfieaľreklrgglihd ipvlpdpttlqernryitvelsnsdtesievgidv tnaywayragtqsyflrdapssasdylftgtdqh slpfygtygdlerwahqsrqqiplglqalthgisf frsggndneekartliviiqmvaeaarfryisnrv Bioinformatika Známé lektiny Y Nové lektiny Levné Online databáze! LectomeXplore - A database of predicted lectins What is LectomeXplore ? LectomeXplore is a module dedicated to the exploration of predicted lectins tor each class from UniLectin3D classification. Translated genomes (proteomes) released in the UniProtKB and RefSeq sequence databases and in the PDB structure database were screened to identify the lectome (complete set of lectins) of the corresponding species. How many predicted lectins ? Proteins with a specific lectin domain: 993249 candidate lectins in 24156 species Workflow of lectin domains prediction 109 lectin classes Lectin 3D structures Conserved 2 5 yC ™5 .., Datasets of I nrntein umiarw-M Web Database protein sequences 4 HMMER Protein sequences identified with a lectin domain profiles Y filtering and cleaning LectomeXplore Predicted lectins in all available species from all kingdoms MycoLec Predicted lectins in fungal genomes htt ps ://www. u n i lect i n. e u/p red i ct/ https://www.unilectin.eu/mycolec/ Identifikace a izolace nových lektinů Práce s komplexním přírodním vzorkem. Malé množství vzorku (např. klíště), drahý vzorek, špatně dostupný. Nízká koncentrace lektinů. Poškození proteinů izolačním procesem. Pionýrský výzkum, rizikový. Nové lektiny s dosud neznámou strukturou/vlastnostmi! Lectin array Lectin affinity chromatography a i"4; Lectin histochemistry SDS-PAGE & Western Blot with lectins Enzyme-linked lectin assay (ELLA) Biological activity Mitogenic Anticancer Necrotic Antibacterial Antiviral XT # Hp @ Antifungal Antihelmintic ^ Nové lektiny ^ Nové unikátní lektiny — Extrakce proteinů Detekce lektinové aktivity Purifikace lektinů GlycoPedia „Glyko drbna" https://www.glycopedia.eu/ Glyko stránky news e-chapters resources search Starch : Structure and Morphology Serge Perez - Anne Imberty Library of Bio-active Monosaccharides. 1D,. Serge Perez 18 mars 2022 Acholetin : A newly discovered Poly 1-3 p-D GlcNAc bacterial polysaccharide Using genomic data and activity-based screening, the researchers identified a glycoside phosphorylase enzyme Acholetin •sphorylase 11 mars 2022 Glycomimetics against Multi-Drug Resistant Pathogens The collection of glycopedia virtual chapters has been extended with a new contribution Multi-drug resistant NMAc NHAc Acholetin fevrier 2022 new Recent Advances in Electron Microscopy of Carbohydrate Nanoparticles Carbohydrate nanoparticles, both naturally denved and synthetic ones, have attracted scientific and ÍPolydUp«nj«y janvier 2022 Chitin and Chitosan in the Bioeconomy Chitin is the second most abundant natural polymer in the world after cellulose, mainly derived from the food.. 20 décembre 2021 news Modernized uniform representation of carbohydrate molecules in the Protein Data Bank Carbohydrate molecules present in more than 14,000 Protein Data Bank (PDB) structures have recently been... Lipidy Lipidy jsou heterogenní skupina biomolekul nerozputných ve vodě a rozpustných v organických rozpouštědlech. Jsou to deriváty vyšších mono karboxylových kyselin a alifatických či alicyklických hydrojíyderivátů nebo aminoderivátů. Patří do ní následující látky: 1. Tuky a oleje facylqiyceroly) 2. Glycerolipidy (glycerofosfolipidy, plasmalogeny, kardiolipin) 3. Sfinqolipidy 14. Steroidy (cholesterol, žlučové kyseliny, steroidní hormony") 5. Izoprenoidy (ubichinon, plastochinon, dolichol) 6. Vitaminy rozpustné v tucích 7. Deriváty mastných kyselin (Jeukotrieny, prostaqlandiny, prostacykliny, trpmbpxany) Lipidy hrají v organismu roli jako zásobní látky, strukturální složky membrán, hormony a vitaminy. 4.8.16 Lipids Small, biologically active molecules of variable structure, commonly defined by their solubility in non-polar solvents. Hydrophobic or amphipathic small molecules that may originate, entirely or in part, by the car banion-based condensations of thioesters (fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids, and polyketides) and/or by carbocation-based condensations of isoprene units (prenol lipids and sterol lipids). Terminology of bioanalytical methods (IUPAC Recommendations 2018) https://doi.org/lO.1515/pac-2016-1120 Received November 21, 2016; accepted February 1, 2018 Základní pojmy z biochemie, V. Mikeš, Katedra biochemie PřF Masarykovy Univerzity v Brně, 2. doplněné vydání 2001 Lipidy a lipidomika * Zásobní látky (zdroj energie), mechanická ochrana, tepelná izolace, hormony, složky membrán, vitaminy Lipidomika Lipidomika je vědní obor, který se zabývá studiem biochemických drah lipidů v biologických systémech. Slovo lipidom označuje veškeré lipidy v buňce, tkáni nebo organismu v daném čase a je podmnožinou metabolomu Lipidomika je relativně mladý obor, který se rozvíjí v souvislosti s rychlými pokroky v lékařství, analytické chemii a informačních technologiích. Lipidy hrají velmi důležité role při vzniku a průběhu mnoha metabolických chorob jako je například obezita, ateroskleróza. cévní mozková příhoda, hypertenze nebo diabetes. V lipidomickém výzkumu se pracuje s velkými soubory dat, které kvantitativně popisují změny v obsahu a složení jednotlivých druhů lipidů. Analýza lipidomu znamená identifikaci a kvantifikaci tisíců molekulárních druhů lipidů, zkoumá se struktura a interakce s dalšími sloučeninami, jejich dynamika a změny, které nastanou v průběhu vzniku choroby Informace získané z těchto studií hrají důležitou roli při objasňování vzniku a průběhu nemocí na molekulární úrovni. ls Lípídomícká sekce České společnosti pro oiocnemii a molekulární biologii http://lipidomics.uochb.cas.cz/lipidomika.html Lipidy Lipidy jsou strukturně různorodé chemické sloučeniny, které plní řadu klíčových biologických funkcí, například jako stavební složky buněčných membrán, zdroje a zásobárny energie, nebo jako signální molekuly. Lipidy mohou být obecně definovány jako hydrofobní nebo amphipatické molekuly, které alespoň částečně vznikají kondenzací thioesterů (mastné kyseliny, polyketidy, atd.) nebo isoprenových jednotek (prenoly, steroly, atd.). Lipidy se obecně dělí na "jednoduché" a "složené" lipidy, přičemž jednoduchými lipidy rozumíme ty, které při hydrolýze poskytují nanejvýš dva typy produktů, kdežto složené lipidy dávají při hodrolýze tri nebo více produktů. Lipidomics: a global approach to lipid analysis in biological systems Andrew D. Watson1 DťparĹiiicľiiL of Medici lie. Division {if Carclif.] Logy. David Cefftu -ScihjoI of Medicine, University of C jli fun tia Ai Lm Angeles. Los Angles, CA 90095 1. How to preserve and extract lipids? 2. What amount of lipids is present in the sample ? 3. How to fractionate a natural lipid extract? i. What are the components present within each fraction? 5. What amounts of each component are present in the lipid extract? General organizations Companies involved in Scientific Research Sites devoted to sciences and techniques Databases and encyclopedia Browsing on the net Discussion Groups Food and Nutrition journals on-line Scientific journals Scientific Societies and organizations Scientific Libraries Publishers Analýza lipidů http://cyberlipid.gerli.com/ Odkazy CYBERLIPID CENTER 1. This site for cyberlipici studies is an online, non-profit scientific organization whose purpose is to collect, study and diffuse information on all aspects of lipidology. 2. The site seeks to establish contacts between students, teachers, scientists and technicians and expose various models in all fields, forgotten studies of the past, work in progress and hot fields. 3. The site will try to feature an extensive, always upgraded, annotated bibliography devoted to the main presented topics, Lipid suppliers Sites directly involved in fat and lipids Journals devoted to lipids Historie 1758 First study by Poulletter de la Salle FP of a lipid (cholesterol) isolated from bile stones. 1779 Discovery by the Swedish scientist Scheele CW of glycerol obtained by heating several oils and fats with lead oxide. 1783 Fourcroy AF introduced alcohol to extract brain lipids. 2022 Kalendář 8-10 March 2022 - 10th International Singapore Lipid Symposium (i S LS10) - Themes of precision health and medicine, nutritional science, healthy longevity, cardiometabolic diseases, infection biology, microbiome and n o ■ =. For information contact: web site 10-15July 2022 - 25th International Symposium on Plant Lipids (ISPL meeting], Grenoble, France For information contact: web site 6-9 November 2022 - The 17th GERLI Lipidomics Meeting "Lipids: from membrane dynamics to signaling" will be held in Saint-Jean-Cap-Ferratr France (on the French RMera, near Nice). For information contact: web site • • • • «3» I LIPID MAPS® Lipidomics Gateway https://www.lipidmaps.org/ Lipid classification, structures and tools4 Eoin Fahy\ Dawn Cotter, Manish Sud, and Shankar Subramaniam University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0411, USA Abstract The study of lipids has developed into a research field of increasing importance as their multiple biological roles in cell bio log}', physio log;- and pathology are becoming better understood. The Lipid Metabolites and Pathways Strategy (LIPID MAPS) consortium is actively invoked in an integrated approach for the detection, quantitation and pathway reconstruction of lipids and related genes and proteins at a systems-biology level. A key component of this approach is a bioiiifomiarics infrastructure involving a clearly defined classification of lipids, a state-of-the-art database system for molecular species and experimental data and a suite of user-friendly tools to assist lipidomics researchers. Herein, we discuss a number of recent developments by the LIPID MAPS bioin forma tics core hi pursuit of these objectives. This article is pait of a Special Issue entitled Lipodomics and Imaging Mass Spectrometry. Lipidy a lipidomika International Lipid Classification and Nomenclature Committee (2005): Klasifikační systém zahrnující 8 hlavních kategorií, každá je dále členěná (třídy podtřídy a někdy podpodtřídy) Lipid of the Month March, 2022 o Sapienic acid Lipid Classification System The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's (LMJD) which reflects their position in the classification hierarchy. LMSD can be searched by lipid class, common name, systematic name or synonym, mass, InChlKey or LIPID MAPS ID with the search box in the banner, or alternatively, by LIPID MAPS ID, systematic or common name, mass, formula, category, main class, subclass data, or structure or sub-structure with one of the search interfaces in the LMSD database section, Each LMSD record contains an image of the molecular structure, common and systematic names, links to external databases, Wikipedia pages (where available), other annotations and links to structure viewing tools. In addition to LMSD search interfaces, you can drill down through the classification hierarchy below to the LMSD record for an individual lipid. Lipidy - strukturní databáze Třídění lipidů a informatika lipidů obecně je, ve srovnání s proteiny a nukleovými kyselinami, poměrně nový obor. LIPID MAPS Structure Database (LMSD) The LIPID MAPS® Structure Database (LMSD) is a relational database encompassing structures and annotations of J>alogically relevant lipids. As of 05/01/2021, LMSD contains ^5684 u}iique lipid structures, making it the largest public ipid-only database in the world. The LIPID MAPS® Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. As of today, LMSD contain^7433^)iique lipid structures, making it the largest pub(it*liptTl-only database in the world. https://www.lipidmaps.org/data/structure/index.php Lipid Category Curated Computationally-generated All Fatty Acyls [FA] 8551 1875 10426 Glycerolipids [GL] 347 7379 7726 Glycerophospholipids [GP] 1725 8312 10037 SphingoLipids [SP] 1784 3168 4952 Sterol Lipids [ST] Prenol Lipids [PR] 3483 2344 0 0 3483 2344 Saccharolipids [SL] 51 1294 1345 Polyketides [PK] 7120 0 7120 TOTAL 25405 22028 47433 Structures of lipids in the database come from several sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT, Lipid Library, Cyberlipids, ChEBI and other public sources; (iv) novel lipids submitted to peer-reviewed journals; (v) computationally generated structures for appropriate classes. Klasifikace podle LIPID MAPS systému Přidělení ID LIPID ID (LM ID) format Characters Position Description LMFAO103OO01 1-2 Database designation LMFA01030001 3-4 Two-letter category code LMFA01030001 5-6 Tmo-disit class code LMFAG1D30001 7-8 Tino-disit subclass code LMFAQ10300D1 9-12 Unique four character identifiedwith in a subclass Lipidy - strukturní databáze • Třídění lipidů a informatika lipidů obecně je, ve srovnání s proteiny a nukleovými kyselinami, poměrně nový obor. • LIPID MAPS Structure Database (LMSD) Structure-based search using GGA Ketcher ^ |100% * I Aran Atem eoA H < C N 0 A+ on S A" lí^l P —_ [ ] Cl >-R1 Br Q 1 Generic Graupa LMSD: Structure-based search results Modify Search 1HJD Common Name Systematic Mame Formula Mass Main Class Sub Class L M PR0103330002 Gossypol (W S ) 518,1941 lsoprenoids[PR01] LIPID MAPS does not verify the accuracy of this Wikipedia entry C15 isoprenoids (sesquiterpenes) [PR0103] Download results CSV T Gossypol Search type LM ID Name(Common, Systematic, or Syno nym) Include Records per page 50 Sort by Substructure * ■♦All records ■. Curated records only' .■Computationally generated records only |so |lm_id 'I From Wikipedia, the free encyclopedia Not to be confused m'tft Gossypetin. Gossypol is a natural phenol derived from trie cotton plant (genus Gossypium). Gossypol is a phenolic aldehyde that permeates cells and acts as an inhibitor for several dehydrogenase enzymes. It is a yellow pigment. Among other things, it has been tested as a male oral contraceptive in China. In addition to its putative contraceptive properties, gossypol has also long been known to possess antimalarial properties.[11 Submit I Reset https://www.lipidmaps.org/ (Bio)informatické nástroje Nástroje pro grafické znázornění lipidů Nástroje pro MS analýzu lipidů Lipid Structure Drawing Tools Mass Spectrometry Tools sn1-Acyl group 20:0 sn2-Acyl group 22:6(4Z,7Z, 10Z, 13Z, 16Z, 19Z) sn3-Acyl group 33:0 Product ion calculation tool foKGIycerolipidsJ/ ion mode) Ion IM+NH4]+ T fn1 20:0 * sn2 22:6(4Z,7Z,10Z,13Z,16Zr19Z) T sni 26:0 1 Submit Reset Submit Reset 1 Commonly occurring product ions for TG(20:0/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/26:0) m/z Ion Description 1092.9893 Precursor ion [M + NH4] + 1075.9527 Precursor ion [M + H]+ 1057.9521 Precursor ion [M + H]+ with loss of H20 763.6599 Neutral loss ofsnl RCOOH + NHS from [M + NH4] + 747.7225 Neutral loss of sn2 RCOOH + NH3 from [M + NH4] + 579.5660 Neutral loss ofsn3 RCOOH + NHS from [M + NH4] + 453.4302 sn3 acyl chain ([RC=0 +74]+} 435.4196 sn3 acyl chain ([RC = 0 +74]+ with loss of H20) 385.2737 sn2 acyl chain ([RC=0 +74]+} 379.3934 sn3 acyl chain [[RC=0]+] 369.3363 snl acyl chain ([RC=0 +74]+} 367.2631 sn2 acyl chain |[RC=0 +74]+ with loss of H20) 361.3829 sn3 acyl chain ([RC=0]+ with loss of H20) 351.3257 snl acyl chain |[RC=0 +74]+ with loss of H20) 311.2369 sn2 acyl chain |[RC=0]+] 295.2995 snl acyl chain |[RC=0]+] 293.2264 sn2 acyl chain ([RC = 0]+ with loss of H20) 277.2890 snl acyl chain ([RC = 0]+ with loss of H20) I C^jycolipids: AnimaT^ľ^ HakomoMSeiwnrTjTi^nrTIJTvDr^^ irar-tfc, Washington, VIA hhizukd Into, fai^Univroity^mfafM^icin^ fcfc^jtuinn Glycol ipkls a ie a rbohydrates linked^ They are found in animal cells and tissues. Advanced article £ I Arttcfc Contents * kitoodudn * + £yn:"tfl!s_ id Ikg-jdj: 4 fUKÜOT ■ ■:«J«m*1 4M1A Sfrutrc. ĎĽ7t*UlMl Hid n j: L5! >n -go id: n M-snty-ST* Introduction GlycolLpids are uhiquLtous componenLs of all animaL cell membranes and are particularLy abundanL at the cell sur-face mem h ran*. I he majority ofglycoLipids belong Lo the class 'glycosphingolipids' {GSLs; aLso called sphingogly-co lipid? ), which have a heck bone lipid (termed 'ceramide') consLSLmg of fatty adds and a long-chain aliphatLC ammo alcohol, discovered and named 'sphingosine" by JLW Tbudiebum in 1S76. Sphingosine has Lhe strueLure 1,3-di-bydroxy-2-amino-ocLadecene, exhibiting ibe o-erytbro sLereoconfiguraLion with regard to Lhe asymmetric carbon ] (C ] ),C2andC3 {Figure la). Fatty adds with va nous chain lengths are linked to the 2-amino group of sphingosine to form ceramide (Figure lb). Various sugar residues are linked to the Cl primary hydro xyl group of the sphingosine moiety in ceramide to form galactosyl ceramide (GalCer) [Figure It), gl ucosylceramide (GlcCer) {Figure Id), or a va-r iety o f mo re comp lex o ligosacchar ides, res u iti ng in a wide variety of GSLs. One example of such a structure, hGM3\ which has sialic acid, galactose and glucose, is shown in Figure 1e. lhe sugar linkage to the CI hydroxy! group of ceramLde ls always j?, with only a single known exce pi ion x-Gal ceramide, which Ls found in sea anemones. GSLs are also found in plants, including yeast, although the ceramide and carbohydrate strucLures aredistinctively differen t fro m rbo seo fan imal GSLs. T he ceramideo f plan t GSLs has a sphingosine analogue, termed 'phylosphingo-sine', which has an additional hydroxy! group at the C4 position. The carbohydrate moiety of plant GSLs has a novel glycan, termed 'pbyLoglyeosphingolipid', ccnsLsling of phospboinositol, glucosamine and mannow_ GSLs are rarely found in bacteria, except for a novel group of 'sphingobacteria' that includes Sphingomonasptxtcintofrilis. A fur there lass of glyco lipids, Lermed 'glyeoglycerolipidsV has been found and characterised. They have ] ,2-dLacyL-.irt-glycerolor 1 alkyl-2-acyl-.hrr-glycerolasabackbonelipid,Lo which a monosaccharide or relatively short oligosaccharide is linked through the primary hydroxy! group (Figure 2). Only m o glycnglyeernlipids have been wellcharacreriTed as animal tissue components. Their disniburion is limited lo the nervous system {brain, spinal cord, peripheral nerves) and testis. Jn contrast to animal tissues, glyco glycerol ipids are the major component in plants and bacteria. do* Id. tt*2/WfiŮ4í»1S»2 j«rtrjř*áp*2 Another class of g lyce roglyco lip id s Ls the 'glycosylpho-s phatidylinosito lane ho r"{Gri anchor). A large number of functionally important cell-surface proteins are anchored through this class of glycoglycerolipids (see helow). See a to: GlycolipLds: disLnbuLion and biological function Structu re The mostextensive studieson LhesLructure and function of animal cell glycolipids have been focused on GSLs. GSLs conslsLofLwo distinct moieties: ceramide, which is hydrophobic, and carbohydrate, which ls hydrophyte. A molecular model of GSL based on X-iay crystallography indicates that the axis of the ceramide is perpendicular to the axis of the carbohydrate chain. GSLs have a strong tendency to aggregate Lo form micelles in aqueous media, or to form mLcrodomaLns in the cell membrane hi Layer. GSLsfromanimaL tLssuesareclassifiedaccording Lo two criteria: f l)tbe presenceorahsenceof sirongly acidic group (s Lalic add or s ulfaLe), o r caUon lc ami no gro u p (vet y r arely pre.senL);and {2)dit7etences incotecarbohydraLe sLrucLure. hour subclasses based on criterion (]) are neuLralGSLs. gangliosides {GSLs conLaining sialic acid), sulfaLide {sulfated GSL) and a few cationic GSLs having free amino group. Three subclasses based onenLenon{2)are: ganglio-series, lacLo-series and globo-series GSLs. In Lhe current LiLeraLure,approximaLely iwganglio-series, So lacLo-series and globo-series GSLs are known. Lot ganglio-series GSLs, 2 neutral, 7 sulfatedand --40 sialylated speciesare known. For laeto-series, 14 neutral, 2 sulfated, — 3D sialylated and —32 fucosylaLed speciesare known. Jn some cases, hyb rid Lypes between Lhe lacLo - and gangl io -se ries o r bet ween the globo- and Lacro-seties have been observed. In certain protoioa,parasitesand marine inverLehraLes,novel GSL structures have been observed that cannot be assigned to any of the thtee subclasses described above. Neutral ylycosphinyolipids The most abundant GSL in animal tissues is galactosyl-cetamide (GalCer, cerebroside) in brain, discovered by Lipidy + sacharidy Antigény Receptory Adheze Lipidová část slouží k ukotvení v membráně Create a Sphingolipid Glycan Structure Core: ^^^^"^CTlffflB^^^^^^^ Core chain style: Straight T Glycan: |Galb1-J(GlcNAcb1-G)GalNAcb1-3Gala1-4Galb1-4Glcb Glycan chain orientation:| Left *j https://www.lipidmaps.org/ Submit Reset Usage Sugar residues allowed: Glc, Gal, Man, GkNAc, GalNAc, Xyl, Flic, NeuAc, NauGc, KDN Glycan sequence must be in the format: [sugar (as an a bbreviation)] [ancmer (either a or b)] [linkage in [x-y form)] Examples: Galb1-4Glcb, Fuca1-2Galb1-3GalNAcb1-4Galb1-4Glcbf NeuAca2-3Galb1-3GalNAcb1-3Gala1-4Galb1-4Glcb Branched glycans are designated by parentheses:GalNAca1-3GalNAcbl-3(Galb1-3GalNAcb1-4)Gala1-4Galb1-4Glcb (The hypothetical structure below contairs al ' 3 sugar resicazi cjrrerdy iLapotedi Ľ HC It LOP [DIA OF LIFL SC1LNCĹS C Stub, til n WWrj iSais. Ltl. Protein AAAAAV Lipidy + proteiny LipoP -1.0 Signal peptidase I & II cleavage sites in gram- bacteria The LipoP 1.0 server produces predictions of lipoproteins and discriminates between lipoprotein signal peptides, other signal peptides and n-terminal membrane helices in Gram-negative bacteria. MINIREVIEWS Lipoproteins of Bacterial Pathogensv A. Kovaci-Simon, R. W. Titbal], and S. L. Michell* Note: Although LipoP 10 has been trained on sequences from Gram-negative bacteria only, the following paper reports that it has a good performance on sequences from Gram-positive bacteria also: Methods for the bioinformatic identification of bacterial lipoproteins encoded in the genomes ot Gram-positive bacteria O. Rahman, S. P. Cummings, D. J. Harrington and I. C. Sutcliffe World Journal of Microbiology and Biotechnology 24(11)2377-2382 (2008) https://services.healthtech. dtu.dk/service. php?LipoP-1.0 PRED-LIPO HKl-ULl PO Prediction of Lipoprotein and Secretory Signal Peptides in Gram-positive Bacteria with Hidden Markov Models We present a Hidden Markov Model method for the prediction of lipoprotein signal peptides of Gram-positive bacteria, trained on a set of 67 experimentally verified lipoproteins. The method outperforms LipoP and the methods based on regular expression patternsr in various data sets containing experimentally characterized lipoproteinsr secretory proteins, proteins with an N-terminal TM segment and cytoplasmic proteins. The method is also very sensitive and specific in the detection of secretory signal peptides and in terms of overall accuracy outperforms even SignalP, which is the top-scoring method for the prediction of signal peptides. Abstract Bacterial lipoproteins are a diverse and functionally important group of proteins that arc amenable to unique signal bioinfomniitie analyses because of their peptide features Here wc have used a dataset of sequences of experimentally verified lipoproteins of Gram-positive bacteria to refine our previously described lipoprotein recognition pattern (G+LPP). Sequenced bacteria] genomes can be screened for putative lipoproteins using the G+LPP pattern. The sequences identified can then be validated using online tools for lipoprotein sequence identification. Wc have used our protein sequence dalascts to evaluate six online ttxils for efficacy of lipoprotein sequence identification. Our analyses demonstrate that LipoP (http://www.cbs.dtu.dV/semces/LipoPiO performs best individually but that a consensus approach, incorporating outputs from predictors of general signal peptide properties, is most informative. http://bioinformatics.biol.uoa.gr/PRED-LIPO/ Všechno souvisí se vším... „Take-home message" Sacharidy: zdroj/zásoba energie, stavební a informační funkce. Na syntéze komplexních glykanů se podílí množství proteinů (genů). Glykosylace je významná posttranslační modifikace (funkce x poruchy x predikce). Lektiny - proteiny, které specificky a reverzibilně vážou sacharidy. Na rozdíl od NA/proteinů se u sacharidů často používá grafické znázornění. Výpočetní nástroje jsou důležité i pro zpracování experimentálních dat. Lipidy nejsou jen zdroj/zásoba energie © Použitá a doporučená literatura Terminology of bioanalytical methods (lUPAC Recommendations 2018) Chem Soc Rev RSC Publishing https://doi.org/10.1515/psi-2016-1120 Received November 21, 2016; accepted Februaryl, 2018 Lectins N 3th OTi 5 hart? a HKrjnnwJji bfc-Li ííi^ij:. JTOomJ, .'fLír1 B-JtúJ.l.n JlMť pOJTůn ŮK pJWüzii rtl-.riti.n ď Alf BKYťtaMfcllJ ůTJ TóHl-n-Lii f ELT :■ .in-iik Lir-tin 3 Jj y N-J.h>Ji ľlur.jn -in-J H.jj'rvj L h REVIEW ARTICLE Evolutionary aspects of ABO blood group in humans Massimo Franchini * Carlo Bon fan ti Department oj Hematology and Trujisjusjorr Mediane. Agenda Qspedatiaa Carlo Pamn. Mnntova. Italy ABSTRACT The antigens of the ABO blood group system (A. B and H determinants) are complex carbohydrate molecules expressed on red blood cells and on a variety of other cell lines and tissues. Crowing evidence is accumulating that ABO antigens, beyond their key role in transfusion medicine, may interplay with the pathogenesis ol many human disorders, including infectious, cardiovascular and neoplastic diseases, in this narrative review, after succinct description of the current knowledge on the association between ABO blood groups and the most severe diseases, we aim to elucidate the pa rticularly intriguing issue of the possible role of ABO system in successful aging. Ln particular, focus will be placed on studies evaluating the ABO phenotype in centenarians [lie best human model of longevity. <© 2015 Bsevier B.V. All rights reserved. ■AvjNjijIs online at www.icwncidJrecl.torn Advanced DRUG DELIVERY Dni; Delivery lí=r *v. < Si ■ 2 i d 1.. 12S 1?J unn.kiu.le y.Lľr Lectin-mediated drug targeting: history and applications Christiane Bies*, Claus-Michael Lebra, John F, WoocUeytv* 11'.i.yu." m.-.'u ^j: ■;-,n.,7,:ii i _:i 2 -• ij.'iif r ,,u.,7,:ii- \-: :\:\■ i[r .Y^j.'JlTiJ ' '."in -.■-.•in .-iji±,-,\,:Y w vi ' :■ /7«i.j.■ r" bwt dr tiiraqi* Jfw Xrirtftairfwi'., Fmi lie dir. frirwxr ffinrniamiB/pinz JO rJwrnm Jr.'. Mam jthtrx. j HH>2 mutaine. r 1-1 Ortíihej m\2- Multivalent glycoconjugates as anti-pathogen it agents! Anna Bernardi,3 J esus Jim énez Barbero,15 Alessandro Casnati,c Cristina De Castro,d Tamis Darbre,c Franck Fieschi* Jukka Finne.9 Horst Funken.h Karl Erich Jaeger.h Martina Lahmann,1 Thisbe K. Lindhorst,-1 Marco Marradi,k Paul Messner,' Antonio Molinaro-,d Paul V. Murphy,m Cristina Nativi," Stefan Oscarson,0 Soledsd Penades,11 Francesco Peri,0 Roland J. Pieters.^ Olivier Renaudet.r Jean Louis Reymond,1 Barbara Richichi,n Javier Rojo,1 Francesco Šansone,11 Christina Schaffer,1 W. Bruce Turnbull,T Trinidad VelascoTo-rrijos,IJ Sébastien Vidal,v Siéphane Vin cent,'* Tom Wen n ekes,* Han Zuilhof* and Anne Imbeny*3 TXJT ]Ů.]Q£rT/i]Ů7]ÍŮ]2.ÍJ*T.y Genomics iuui cpigcnomics of the human gJvťomc- \ lacks /.iřliJíř- - "^1 i-I a ■■ Vru iřkiuLT ■ h-mia liiiľIilIí ■ C I'M iJ Uli i. U li ľ New insights into influenza A specificity: an evolution of paradigms Ye Ji, Yohanna JB White, Jodi A Hadden1, Oliver C Grant and Robert J Woods Feng Li'-2, Olga V. Glinskii'-3 and Vladislav V. Glinsky'-2 Proteomics 2013, Í3.341-354 DOI 10.1002/prnic.201200149 Essentials of Glycobiology Technical Note SugarSketcher: Quick and Intuitive Online Glycan Drawing Davide Aloccí i,1r Pavla Suchánková 3r4, Renaud Costa 5, Nicolas Hory s, Julien Mariethoz 'i-Ra d ka Svobodová Var eková ! ■*, Fh LI i p Toukach. * and Pre d éňq ue L i 5 ace k 1 ■ ^' * Host cell recognition by the henipaviruses: Crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3 Kai Xu*. Kan agalag hatta R. Rajashankar', Yee-Peng Chan', Juha P. Himanen*, Christopher C. Broder', and Dimitar B. Nikolov* •Structural Biology Program. Memorial Sloan- Kettering Cancer Center, 1275 York Avenue. New York. NY 10021, 'Northeastern Collaborative Access 1 Použitá a doporučená literatura Glycoproteins Tony Merry, University ofManchester, Manchester, UK Sviatlana AstrautSOVa, Grodno State Medical University, Grodno, Belarus Based in part on the previous version of this Encyclopedia of Life Sciences (ELS) article, "Glycoproteins"by "Terry DButters". Glycolipids: Animal H ako mori Sen-itiroh> ŕWiL NnňrmatRexan^^tuteandlinfi^nitynfWaAirigtiin, !m(-Uer WoífiínplDn, U'iA líhíiuka ln*?0, ľŕifyi Untn^ity Irŕirof ulMadiuTW, 7nt\rBr fapan GlyculiprdsarearbohydralEslinke^^ in animal cells and tissues. Advanced article !;-ví!! i-id klidil si 01| j 'i /j; ľ 'i -= w -: ■ "ij ■ :■ j ■■ "--i .■-,>- j Ed.lrd by Hwiijwchim Cabiut ^ I The Sugar Code Fundamentals of Glycosciences Essentials of Glycobiology Lipid classification, structures and tools* Eoin Fahy*, Dawn Cotter, Manish Sud, and Shankar Subramaniam University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0411; USA MINIREVIEWS Lipoproteins of Bacterial Pathogensv A. Kovacs-Simon, R. W. Titball, and S. L. Michell" Kazuistika dívky s dědičnou poruchou gly kosy lace MUDr. Martin Magner, Ing. Kateřina Veselá, RNDr. Hana Hansíkcvá, CSc, prof. MUDr. Jiří Zeman, DrSc, MUDr. Tomáš Honzík, Ph.D. Klinika dětského a dorostového lékařství, 1. Lf UK a VFN Praha Building and rebuilding N-glycans in protein structure models Identification of novel N-glycosylation sites at non-canonical protein consensus motifs Mark S. Lowenthal". Kiersta S. Davis Trina Forniolo, Lisa E. Kilpatrick. and Karen W. Phinney Bart van Bťusťknm,'1 Mala s ja Wezel/1 Maarlen L. Heltkelman,'* Anaslassis Perrdli1srJ Paul Emsleyb Eind Robbie P. Joosten** Blood Groups j-..! Red Cell Antigens LMM Lipidomics: a global approach to lipid analysis in biological systems Andrew D. Watson1 Department of Medicine, Division uf i]artliuLogv. David (ieffe-u Sclioul of Medicine, University of California at Lm Angeles. Los Angeles, CA 90095 Sweet new world: glycoproteins in bacterial pathogens M. Alexander Schmidt1, Lee W. Riley2 and Inga Etenz1 I Immunity. School of Public Health. University of California. 140 Warren Hall. Bsitaley