Carbohydrates
Abstract
Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called “sugar code,” just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).
Keywords
Carbohydrates Sugars Glycans Biomolecular interactions Non-covalent interactions Hydrogen bonding Conformations Micro-hydration Gas-phase spectroscopyNotes
Acknowledgements
Professor John P. Simons has pioneered the study of neutral CBHs in the gas phase. Several “generations” of students and post-docs have been lucky enough to spend some time in his group. We had the opportunity to contribute to very exciting studies and, most importantly, we found inspiration and confidence to pursue our own scientific interests. John has been especially important for the two of us for developing our own activities and we can never thank him enough for his support. We also want to thank all our friends from the “JPS sugar team” who contributed over the years. Francis Talbot, Rebeccah A. Jockush, Niel A. Macleod, Isabel Hunig, Cristina Stanca-Kaposta, Bo Liu, Timothy D. Vaden, Zheng Su, Nitzan Mayorkas, and Svemir Rudic.
References
- 1.Varki A (1993) Glycobiology 3(2):97–130Google Scholar
- 2.Berg JM, Tymoczko JL, Stryer L (2002) Carbohydrates. In: Biochemistry, 5th edn. W.H. Freeman, New YorkGoogle Scholar
- 3.Taylor ME, Drickamer K (2003) Introduction to glycobiology, 2nd edn. Oxford University Press, London, New YorkGoogle Scholar
- 4.Rudd PM, Dwek RA (2006) Curr Opin Struct Biol 16(5):559–560Google Scholar
- 5.Imperiali B (2012) J Am Chem Soc 134(43):17835–17839Google Scholar
- 6.A Roadmap for the Future (2012) National Research Council (US) committee on assessing the importance and impact of glycomics and glycosciences. National Academies Press, Washington. ISBN-13: 978-0-309-26083-1-ISBN-10: 0-309-26083-3Google Scholar
- 7.Simons JP, Jockusch RA, Carcabal P, Hung I, Kroemer RT, Macleod NA, Snoek LC (2005) Int Rev Phys Chem 24(3–4):489–531Google Scholar
- 8.Simons JP (2009) Mol Phys 107(23–24):2435–2458Google Scholar
- 9.Schwarz F, Aebi M (2011) Curr Opin Struct Biol 21(5):576–582Google Scholar
- 10.Arnold JN, Wormald MR, Sim RB, Rudd PM, Dwek RA (2007) Annu Rev Immunol 25:21–50Google Scholar
- 11.Wormald MR, Dwek RA (1999) Structure 7(7):R155–R160Google Scholar
- 12.Wormald MR, Petrescu AJ, Pao YL, Glithero A, Elliott T, Dwek RA (2002) Chem Rev 102(2):371–386Google Scholar
- 13.O’Connor SE, Imperiali B (1996) Chem Biol 3(10):803–812Google Scholar
- 14.O’Connor SE, Imperiali B (1998) Chem Biol 5(8):427–437Google Scholar
- 15.Weerapana E, Imperiali B (2006) Glycobiology 16(6):91r–101rGoogle Scholar
- 16.Woods RJ, Pathiaseril A, Wormald MR, Edge CJ, Dwek RA (1998) Eur J Biochem 258(2):372–386Google Scholar
- 17.Bosques CJ, Tschampel SM, Woods RJ, Imperiali B (2004) J Am Chem Soc 126(27):8421–8425Google Scholar
- 18.Gabius HJ (2000) Naturwissenschaften 87(3):108–121Google Scholar
- 19.Gabius H-J, André S, Kaltner H, Siebert H-C (2002) Biochim Biophys Acta Gen Subj 1572(2–3):165–177Google Scholar
- 20.Gabius H-J, André S, Jiménez-Barbero J, Romero A, Solís D (2011) Trends Biochem Sci 36(6):298–313Google Scholar
- 21.Pilobello KT, Mahal LK (2007) Curr Opin Chem Biol 11(3):300–305Google Scholar
- 22.Feizi T, Chai W (2004) Nat Rev Mol Cell Biol 5(7):582–588Google Scholar
- 23.Davis BG (2000) Chem Ind, pp. 134–138Google Scholar
- 24.Shriver Z, Raguram S, Sasisekharan R (2004) Nat Rev Drug Discov 3(10):863–873Google Scholar
- 25.Ernst B, Magnani JL (2009) Nat Rev Drug Discov 8(8):661–677Google Scholar
- 26.Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR, Hart GW, Etzler ME (eds) (2009) Essential in glycobiology, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
- 27.Weis WI, Drickamer K (1996) Annu Rev Biochem 65(1):441–473Google Scholar
- 28.Bertozzi CR, Rabuka D (2009) Structural basis of glycan diversity. In: Varki A, Cummings RD, Esko JD et al (eds) Essentials of glycobiology, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
- 29.Breslow R (2012) J Am Chem Soc 134(16):6887–6892Google Scholar
- 30.Ruiz-Mirazo K, Briones C, de la Escosura A (2014) Chem Rev 114(1):285–366Google Scholar
- 31.Cocinero EJ, Lesarri A, Ecija P, Basterretxea FJ, Grabow J-U, Fernandez JA, Castano F (2012) Angew Chem Int Ed 51(13):3119–3124Google Scholar
- 32.Talbot FO, Simons JP (2002) Phys Chem Chem Phys 4(15):3562–3565Google Scholar
- 33.Jockusch RA, Kroemer RT, Talbot FO, Simons JP (2003) J Phys Chem A 107(49):10725–10732Google Scholar
- 34.Jockusch RA, Kroemer RT, Talbot FO, Snoek LC, Carcabal P, Simons JP, Havenith M, Bakker JM, Compagnon I, Meijer G, von Helden G (2004) J Am Chem Soc 126(18):5709–5714Google Scholar
- 35.Carcabal P, Jockusch RA, Hunig I, Snoek LC, Kroemer RT, Davis BG, Gamblin DP, Compagnon I, Oomens J, Simons JP (2005) J Am Chem Soc 127(32):11414–11425Google Scholar
- 36.Carcabal P, Hunig I, Gamblin DP, Liu B, Jockusch RA, Kroemer RT, Snoek LC, Fairbanks AJ, Davis BG, Simons JP (2006) J Am Chem Soc 128(6):1976–1981Google Scholar
- 37.Jockusch RA, Talbot FO, Rogers PS, Simone MI, Fleet GWJ, Simons JP (2006) J Am Chem Soc 128(51):16771–16777Google Scholar
- 38.Macleod NA, Johannessen C, Hecht L, Barron LD, Simons JP (2006) Int J Mass Spectrom 253(3):193–200Google Scholar
- 39.Screen J, Stanca-Kaposta EC, Gamblin DP, Liu B, Macleod NA, Snoek LC, Davis BG, Simons JP (2007) Angew Chem Int Ed 46(20):3644–3648Google Scholar
- 40.Cocinero EJ, Stanca-Kaposta EC, Scanlan EM, Gamblin DP, Davis BG, Simons JP (2008) Chem Eur J 14(29):8947–8955Google Scholar
- 41.Simons JP, Stanca-Kaposta EC, Cocinero EJ, Liu B, Davis BG, Gamblin DP, Kroemer RT (2008) Phys Scr 78(5), 058124Google Scholar
- 42.Cocinero EJ, Gamblin DP, Davis BG, Simons JP (2009) J Am Chem Soc 131(31):11117–11123Google Scholar
- 43.Simons JP, Davis BG, Cocinero EJ, Gamblin DP, Stanca-Kaposta EC (2009) Tetrahedron-Asymmetry 20(6–8):718–722Google Scholar
- 44.Su Z, Cocinero EJ, Stanca-Kaposta EC, Davis BG, Simons JP (2009) Chem Phys Lett 471(1–3):17–21Google Scholar
- 45.Drouin L, Stanca-Kaposta EC, Saundh P, Fairbanks AJ, Kemper S, Claridge TDW, Simons JP (2009) Chem Eur J 15(16):4057–4069Google Scholar
- 46.Su Z, Wagner B, Cocinero EJ, Ernst B, Simons JP (2009) Chem Phys Lett 477(4–6):365–368Google Scholar
- 47.Brauer B, Pincu M, Buch V, Bar I, Simons JP, Gerber RB (2011) J Phys Chem A 115(23):5859–5872Google Scholar
- 48.Cocinero EJ, Carcabal P, Vaden TD, Davis BG, Simons JP (2011) J Am Chem Soc 133(12):4548–4557Google Scholar
- 49.Cocinero EJ, Carcabal P, Vaden TD, Simons JP, Davis BG (2011) Nature 469(7328):76–U1400Google Scholar
- 50.Jin L, Simons JP, Gerber RB (2011) Chem Phys Lett 518:49–54Google Scholar
- 51.Mayorkas N, Rudic S, Cocinero EJ, Davis BG, Simons JP (2011) Phys Chem Chem Phys 13(41):18671–18678Google Scholar
- 52.Mayorkas N, Rudic S, Davis BG, Simons JP (2011) Chem Sci 2(6):1128–1134Google Scholar
- 53.Pincu M, Cocinero EJ, Mayorkas N, Brauer B, Davis BG, Gerber RB, Simons JP (2011) J Phys Chem A 115(34):9498–9509Google Scholar
- 54.Jin L, Simons JP, Gerber RB (2012) J Phys Chem A 116(46):11088–11094Google Scholar
- 55.Sagar R, Rudic S, Gamblin DP, Scanlan EM, Vaden TD, Odell B, Claridge TDW, Simons JP, Davis BG (2012) Chem Sci 3(7):2307–2313Google Scholar
- 56.H-b X, Jin L, Rudic S, Simons JP, Gerber RB (2012) J Phys Chem B 116(16):4851–4859Google Scholar
- 57.Barry CS, Cocinero EJ, Carcabal P, Gamblin DP, Stanca-Kaposta EC, Remmert SM, Fernández Alonso MdC, Rudic S, Simons JP, Davis BG (2013) J Am Chem Soc 135(45):16895–16903Google Scholar
- 58.Carcabal P, Cocinero EJ, Simons JP (2013) Chem Sci 4(4):1830–1836Google Scholar
- 59.Stanca-Kaposta EC, Carcabal P, Cocinero EJ, Hurtado P, Simons JP (2013) J Phys Chem B 117(27):8135–8142Google Scholar
- 60.Polfer NC, Valle JJ, Moore DT, Oomens J, Eyler JR, Bendiak B (2006) Anal Chem 78(3):670–679Google Scholar
- 61.Stefan SE, Eyler JR (2009) Anal Chem 81(3):1224–1227Google Scholar
- 62.Cagmat EB, Szczepanski J, Pearson WL, Powell DH, Eyler JR, Polfer NC (2010) Phys Chem Chem Phys 12(14):3474–3479Google Scholar
- 63.Stefan SE, Eyler JR (2010) Int J Mass Spectrom 297(1–3):96–101Google Scholar
- 64.Brown DJ, Stefan SE, Berden G, Steill JD, Oomens J, Eyler JR, Bendiak B (2011) Carbohydr Res 346(15):2469–2481Google Scholar
- 65.Stefan SE, Ehsan M, Pearson WL, Aksenov A, Boginski V, Bendiak B, Eyler JR (2011) Anal Chem 83(22):8468–8476Google Scholar
- 66.Contreras CS, Polfer NC, Oomens J, Steill JD, Bendiak B, Eyler JR (2012) Int J Mass Spectrom 330:285–294Google Scholar
- 67.Rudic S, Xie H-b, Gerber RB, Simons JP (2012) Mol Phys 110(15–16):1609–1615Google Scholar
- 68.Pena I, Mata S, Martin A, Cabezas C, Daly AM, Alonso JL (2013) Phys Chem Chem Phys 15(41):18243–18248Google Scholar
- 69.Cocinero EJ, Lesarri A, Ecija P, Cimas A, Davis BG, Basterretxea FJ, Fernandez JA, Castano F (2013) J Am Chem Soc 135(7):2845–2852Google Scholar
- 70.Bermudez C, Pena I, Cabezas C, Daly AM, Alonso JL (2013) Chemphyschem 14(5):893–895Google Scholar
- 71.Peña I, Cocinero EJ, Cabezas C, Lesarri A, Mata S, Écija P, Daly AM, Cimas Á, Bermúdez C, Basterretxea FJ, Blanco S, Fernández JA, López JC, Castaño F, Alonso JL (2013) Angew Chem Int Ed:n/a–n/a 52(45):11840–11845Google Scholar
- 72.Motiyenko RA, Alekseev EA, Dyubko SF, Lovas FJ (2006) J Mol Spectrosc 240(1):93–101Google Scholar
- 73.Foley BL, Tessier MB, Woods RJ (2012) Wiley Interdiscip Rev: Comput Mol Sci 2(4):652–697Google Scholar
- 74.Hansen HS, Hünenberger PH (2011) J Comput Chem 32(6):998–1032Google Scholar
- 75.Kirschner KN, Yongye AB, Tschampel SM, González-Outeiriño J, Daniels CR, Foley BL, Woods RJ (2008) J Comput Chem 29(4):622–655Google Scholar
- 76.Mackerell AD (2004) J Comput Chem 25(13):1584–1604Google Scholar
- 77.Damm W, Frontera A, Tirado–Rives J, Jorgensen WL (1997) J Comput Chem 18(16):1955–1970Google Scholar
- 78.Reiling S, Schlenkrich M, Brickmann J (1996) J Comput Chem 17(4):450–468Google Scholar
- 79.Woods RJ, Dwek RA, Edge CJ, Fraserreid B (1995) J Phys Chem 99(11):3832–3846Google Scholar
- 80.Sameera WMC, Pantazis DA (2012) J Chem Theory Comput 8(8):2630–2645Google Scholar
- 81.Halgren TA (1999) J Comput Chem 20(7):730–748Google Scholar
- 82.Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) J Phys Chem B 105(28):6474–6487Google Scholar
- 83.Kratzcr A (1920) Z Phys 3:460Google Scholar
- 84.Loomis FW (1920) Astrophys J 62:248Google Scholar
- 85.Edward JT (1955) Chem Ind 1102–1104Google Scholar
- 86.Wang C, Ying F, Wu W, Mo Y (2011) J Am Chem Soc 133(34):13731–13736Google Scholar
- 87.Mo Y (2010) Nat Chem 2(8):666–671Google Scholar
- 88.Asensio JL, Jimenez-Barbero J (1995) Biopolymers 35(1):55–73Google Scholar
- 89.Cheetham NWH, Dasgupta P, Ball GE (2003) Carbohydr Res 338(9):955–962Google Scholar
- 90.Larsson EA, Staaf M, Söderman P, Höög C, Widmalm G (2004) J Phys Chem A 108(18):3932–3937Google Scholar
- 91.Martín-Pastor M, Canales A, Corzana F, Asensio JL, Jiménez-Barbero J (2005) J Am Chem Soc 127(10):3589–3595Google Scholar
- 92.Olsson U, Serianni AS, Stenutz R (2008) J Phys Chem B 112(14):4447–4453Google Scholar
- 93.Pincu M, Gerber RB (2012) Chem Phys Lett 531:52–58Google Scholar
- 94.Zierke M, Smieško M, Rabbani S, Aeschbacher T, Cutting B, Allain FHT, Schubert M, Ernst B (2013) J Am Chem Soc 135(36):13464–13472Google Scholar
- 95.Mons M, Dimicoli I, Piuzzi F (2002) Int Rev Phys Chem 21(1):101–135Google Scholar
- 96.Mons M, Piuzzi F, Dimicoli I, Zehnacker A, Lahmani F (2000) Phys Chem Chem Phys 2(22):5065–5070Google Scholar
- 97.Cabezas C, Pena I, Daly AM, Alonso JL (2013) Chem Commun 49(92):10826–10828Google Scholar
- 98.Alonso JL, Lozoya MA, Pena I, Lopez JC, Cabezas C, Mata S, Blanco S (2014) Chem Sci 5(2):515–522Google Scholar
- 99.Brown GG, Dian BC, Douglass KO, Geyer SM, Shipman ST, Pate BH (2008) Rev Sci Instrum 79(5), 053103Google Scholar
- 100.Zaleski DP, Neill JL, Muckle MT, Seifert NA, Carroll PB, Weaver SLW, Pate BH (2012) J Mol Spectrosc 280:68–76Google Scholar
- 101.Neill JL, Harris BJ, Steber AL, Douglass KO, Plusquellic DF, Pate BH (2013) Opt Express 21(17):19743–19749Google Scholar
- 102.Santana AG, Jiménez-Moreno E, Gómez AM, Corzana F, González C, Jiménez-Oses G, Jiménez-Barbero J, Asensio JL (2013) J Am Chem Soc 135(9):3347–3350Google Scholar
- 103.Haseley SR, Vermeer HJ, Kamerling JP, Vliegenthart JFG (2001) Proc Natl Acad Sci 98(16):9419–9424Google Scholar
- 104.Carvalho de Souza A, Ganchev D, Snel ME, Eerden JJM, Vliegenthart JG, Kamerling J (2009) Glycoconj J 26(4):457–465Google Scholar
- 105.Gerhards M, Unterberg C, Gerlach A, Jansen A (2004) Phys Chem Chem Phys 6(10):2682–2690Google Scholar
- 106.Fukui K, Takahashi K (2012) Anal Chem 84(5):2188–2194Google Scholar
- 107.Pagel K, Harvey DJ (2013) Anal Chem 85(10):5138–5145Google Scholar
- 108.Brown LJ, Creaser CS (2013) Curr Anal Chem 9(2):192–198Google Scholar
- 109.Bellina B, Compagnon I, MacAleese L, Chirot F, Lemoine J, Maitre P, Broyer M, Antoine R, Kulesza A, Mitric R, Bonacic-Koutecky V, Dugourd P (2012) Phys Chem Chem Phys 14(32):11433–11440Google Scholar
- 110.Hernandez O, Isenberg S, Steinmetz V, Glish G, Maitre P (2014) Submitted for publicationGoogle Scholar
- 111.Schindler B, Joshi J, Allouche A-R, Simon D, Chambert S, Brites V, Gaigeot M-P, Compagnon I (2014) Phys Chem Chem Phys 16:22131–22138Google Scholar
- 112.Stearns JA, Seaiby C, Boyarkin OV, Rizzo TR (2009) Phys Chem Chem Phys 11(1):125–132Google Scholar
- 113.Shafizadeh N, Ha-Thi MH, Soep B, Gaveau MA, Piuzzi F, Pothier C (2011) J Chem Phys 135(11):114303Google Scholar