CH/π Interactions in Carbohydrate Recognition

Overview

Journal Molecules

Publisher MDPI

Specialty Biology

Date 2017 Jun 24

PMID 28644385

Citations 49

Authors

Vojtech Spiwok

Affiliations

Soon will be listed here.

Abstract

Many carbohydrate-binding proteins contain aromatic amino acid residues in their binding sites. These residues interact with carbohydrates in a stacking geometry via CH/π interactions. These interactions can be found in carbohydrate-binding proteins, including lectins, enzymes and carbohydrate transporters. Besides this, many non-protein aromatic molecules (natural as well as artificial) can bind saccharides using these interactions. Recent computational and experimental studies have shown that carbohydrate-aromatic CH/π interactions are dispersion interactions, tuned by electrostatics and partially stabilized by a hydrophobic effect in solvated systems.

Citing Articles

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References

Jimenez-Moreno E, Jimenez-Oses G, Gomez A, Santana A, Corzana F, Bastida A . A thorough experimental study of CH/π interactions in water: quantitative structure-stability relationships for carbohydrate/aromatic complexes. Chem Sci. 2017; 6(11):6076-6085. PMC: 5504637. DOI: 10.1039/c5sc02108a. View

Asensio J, Siebert H, Von der Lieth C, Laynez J, Bruix M, Soedjanaamadja U . NMR investigations of protein-carbohydrate interactions: studies on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on hevein domains. Determination of the NMR structure of the.... Proteins. 2000; 40(2):218-36. View

cerny J, Vondrasek J, Hobza P . Loss of dispersion energy changes the stability and folding/unfolding equilibrium of the Trp-cage protein. J Phys Chem B. 2009; 113(16):5657-60. DOI: 10.1021/jp9004746. View

Murray A, Chen W, Antonopoulos A, Hanson S, Wiseman R, Dell A . Enhanced Aromatic Sequons Increase Oligosaccharyltransferase Glycosylation Efficiency and Glycan Homogeneity. Chem Biol. 2015; 22(8):1052-62. PMC: 4546532. DOI: 10.1016/j.chembiol.2015.06.017. View

Raju R, Ramraj A, Hillier I, Vincent M, Burton N . Carbohydrate-aromatic pi interactions: a test of density functionals and the DFT-D method. Phys Chem Chem Phys. 2009; 11(18):3411-6. DOI: 10.1039/b822877a. View

Eschenmoser A . Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective. Angew Chem Int Ed Engl. 2011; 50(52):12412-72. DOI: 10.1002/anie.201103672. View

Merritt E, Kuhn P, Sarfaty S, Erbe J, Holmes R, Hol W . The 1.25 A resolution refinement of the cholera toxin B-pentamer: evidence of peptide backbone strain at the receptor-binding site. J Mol Biol. 1998; 282(5):1043-59. DOI: 10.1006/jmbi.1998.2076. View

Asensio J, Arda A, Canada F, Jimenez-Barbero J . Carbohydrate-aromatic interactions. Acc Chem Res. 2012; 46(4):946-54. DOI: 10.1021/ar300024d. View

Bhoi V, Kumar S, Murthy C . The self-assembly and aqueous solubilization of [60]fullerene with disaccharides. Carbohydr Res. 2012; 359:120-7. DOI: 10.1016/j.carres.2012.07.010. View

10.

Huber R, Hakda S, Cheng C, Cupples C, Edwards R . Trp-999 of beta-galactosidase (Escherichia coli) is a key residue for binding, catalysis, and synthesis of allolactose, the natural lac operon inducer. Biochemistry. 2003; 42(6):1796-803. DOI: 10.1021/bi0270642. View

11.

Kim O, Je J, Baldwin J, Kooi S, Pehrsson P, Buckley L . Solubilization of single-wall carbon nanotubes by supramolecular encapsulation of helical amylose. J Am Chem Soc. 2003; 125(15):4426-7. DOI: 10.1021/ja029233b. View

12.

Robert X, Haser R, Gottschalk T, Ratajczak F, Driguez H, Svensson B . The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs. Structure. 2003; 11(8):973-84. DOI: 10.1016/s0969-2126(03)00151-5. View

13.

Fernandez-Alonso M, Canada F, Jimenez-Barbero J, Cuevas G . Molecular recognition of saccharides by proteins. Insights on the origin of the carbohydrate-aromatic interactions. J Am Chem Soc. 2005; 127(20):7379-86. DOI: 10.1021/ja051020+. View

14.

Hanwell M, Curtis D, Lonie D, Vandermeersch T, Zurek E, Hutchison G . Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform. 2012; 4(1):17. PMC: 3542060. DOI: 10.1186/1758-2946-4-17. View

15.

Santana A, Jimenez-Moreno E, Gomez A, Corzana F, Gonzalez C, Jimenez-Oses G . A dynamic combinatorial approach for the analysis of weak carbohydrate/aromatic complexes: dissecting facial selectivity in CH/π stacking interactions. J Am Chem Soc. 2013; 135(9):3347-50. DOI: 10.1021/ja3120218. View

16.

Guerin D, Lascombe M, Costabel M, Souchon H, Lamzin V, Beguin P . Atomic (0.94 A) resolution structure of an inverting glycosidase in complex with substrate. J Mol Biol. 2002; 316(5):1061-9. DOI: 10.1006/jmbi.2001.5404. View

17.

Besombes S, Mazeau K . Molecular dynamics simulations of a guaiacyl beta-O-4 lignin model compound: examination of intramolecular hydrogen bonding and conformational flexibility. Biopolymers. 2004; 73(3):301-15. DOI: 10.1002/bip.10587. View

18.

Juers D, Heightman T, Vasella A, McCarter J, Mackenzie L, Withers S . A structural view of the action of Escherichia coli (lacZ) beta-galactosidase. Biochemistry. 2001; 40(49):14781-94. DOI: 10.1021/bi011727i. View

19.

Jimenez-Moreno E, Gomez A, Bastida A, Corzana F, Jimenez-Oses G, Jimenez-Barbero J . Modulating weak interactions for molecular recognition: a dynamic combinatorial analysis for assessing the contribution of electrostatics to the stability of CH-π bonds in water. Angew Chem Int Ed Engl. 2015; 54(14):4344-8. DOI: 10.1002/anie.201411733. View

20.

Wohlert J, Schnupf U, Brady J . Free energy surfaces for the interaction of D-glucose with planar aromatic groups in aqueous solution. J Chem Phys. 2010; 133(15):155103. PMC: 2980541. DOI: 10.1063/1.3496997. View