1
|
Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations. Int J Biol Macromol 2020; 157:1-9. [DOI: 10.1016/j.ijbiomac.2020.03.251] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/12/2020] [Accepted: 03/30/2020] [Indexed: 02/03/2023]
|
2
|
Houser J, Kozmon S, Mishra D, Hammerová Z, Wimmerová M, Koča J. The CH-π Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification. Chemistry 2020; 26:10769-10780. [PMID: 32208534 DOI: 10.1002/chem.202000593] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/18/2020] [Indexed: 12/16/2022]
Abstract
The molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell, and cell-cell adhesion (e.g., in cancer metastasis). Carbohydrates interact with proteins mainly through hydrogen bonding, metal-ion-mediated interaction, and non-polar dispersion interactions. The role of dispersion-driven CH-π interactions (stacking) in protein-carbohydrate recognition has been underestimated for a long time considering the polar interactions to be the main forces for saccharide interactions. However, over the last few years it turns out that non-polar interactions are equally important. In this study, we analyzed the CH-π interactions employing bioinformatics (data mining, structural analysis), several experimental (isothermal titration calorimetry (ITC), X-ray crystallography), and computational techniques. The Protein Data Bank (PDB) has been used as a source of structural data. The PDB contains over 12 000 protein complexes with carbohydrates. Stacking interactions are very frequently present in such complexes (about 39 % of identified structures). The calculations and the ITC measurement results suggest that the CH-π stacking contribution to the overall binding energy ranges from 4 up to 8 kcal mol-1 . All the results show that the stacking CH-π interactions in protein-carbohydrate complexes can be considered to be a driving force of the binding in such complexes.
Collapse
Affiliation(s)
- Josef Houser
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Stanislav Kozmon
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.,Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538, Bratislava, Slovak Republic
| | - Deepti Mishra
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Zuzana Hammerová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic.,Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Jaroslav Koča
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| |
Collapse
|
3
|
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.
Collapse
|
4
|
Nishio M, Umezawa Y, Fantini J, Weiss MS, Chakrabarti P. CH-π hydrogen bonds in biological macromolecules. Phys Chem Chem Phys 2015; 16:12648-83. [PMID: 24836323 DOI: 10.1039/c4cp00099d] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
Collapse
Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338, Minamioya, Machida-shi, Tokyo 194-0031, Japan.
| | | | | | | | | |
Collapse
|
5
|
Moonens K, Van den Broeck I, De Kerpel M, Deboeck F, Raymaekers H, Remaut H, De Greve H. Structural and functional insight into the carbohydrate receptor binding of F4 fimbriae-producing enterotoxigenic Escherichia coli. J Biol Chem 2015; 290:8409-19. [PMID: 25631050 DOI: 10.1074/jbc.m114.618595] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) strains are important causes of intestinal disease in humans and lead to severe production losses in animal farming. A range of fimbrial adhesins in ETEC strains determines host and tissue tropism. ETEC strains expressing F4 fimbriae are associated with neonatal and post-weaning diarrhea in piglets. Three naturally occurring variants of F4 fimbriae (F4ab, F4ac, and F4ad) exist that differ in the primary sequence of their major adhesive subunit FaeG, and each features a related yet distinct receptor binding profile. Here the x-ray structure of FaeGad bound to lactose provides the first structural insight into the receptor specificity and mode of binding by the poly-adhesive F4 fimbriae. A small D'-D″-α1-α2 subdomain grafted on the immunoglobulin-like core of FaeG hosts the carbohydrate binding site. Two short amino acid stretches Phe(150)-Glu(152) and Val(166)-Glu(170) of FaeGad bind the terminal galactose in the lactosyl unit and provide affinity and specificity to the interaction. A hemagglutination-based assay with E. coli expressing mutant F4ad fimbriae confirmed the elucidated co-complex structure. Interestingly, the crucial D'-α1 loop that borders the FaeGad binding site adopts a different conformation in the two other FaeG variants and hints at a heterogeneous binding pocket among the FaeG serotypes.
Collapse
Affiliation(s)
- Kristof Moonens
- From the Structural and Molecular Microbiology, VIB Structural Biology Research Center, 1050 Brussels, the Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, and
| | - Imke Van den Broeck
- From the Structural and Molecular Microbiology, VIB Structural Biology Research Center, 1050 Brussels, the Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, and
| | - Maia De Kerpel
- From the Structural and Molecular Microbiology, VIB Structural Biology Research Center, 1050 Brussels, the Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, and
| | - Francine Deboeck
- the Viral Genetics Laboratory, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Hanne Raymaekers
- From the Structural and Molecular Microbiology, VIB Structural Biology Research Center, 1050 Brussels, the Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, and
| | - Han Remaut
- From the Structural and Molecular Microbiology, VIB Structural Biology Research Center, 1050 Brussels, the Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, and
| | - Henri De Greve
- From the Structural and Molecular Microbiology, VIB Structural Biology Research Center, 1050 Brussels, the Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, and
| |
Collapse
|
6
|
Liu FY, Long ZW, Tan XF, Long B. Theoretical investigation on mechanisms and kinetics of the reactions of Cl atom with CH3OOH and CH3CH2OOH. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
7
|
Kumari M, Sunoj RB, Balaji PV. Exploration of CH⋯π mediated stacking interactions in saccharide: aromatic residue complexes through conformational sampling. Carbohydr Res 2012; 361:133-40. [DOI: 10.1016/j.carres.2012.08.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/20/2012] [Accepted: 08/28/2012] [Indexed: 11/26/2022]
|
8
|
Kumari M, Sunoj RB, Balaji PV. Conformational mapping and energetics of saccharide–aromatic residue interactions: implications for the discrimination of anomers and epimers and in protein engineering. Org Biomol Chem 2012; 10:4186-200. [DOI: 10.1039/c2ob25182e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
9
|
Kozmon S, Matuška R, Spiwok V, Koča J. Dispersion interactions of carbohydrates with condensate aromatic moieties: theoretical study on the CH-π interaction additive properties. Phys Chem Chem Phys 2011; 13:14215-22. [PMID: 21755090 DOI: 10.1039/c1cp21071h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this article we present the first systematic study of the additive properties (i.e. degree of additivity) of the carbohydrate-aromatic moiety CH-π dispersion interaction. The additive properties were studied on the β-D-glucopyranose, β-D-mannopyranose and α-L-fucopyranose complexes with the naphthalene molecule by comparing the monodentate (single CH-π) and bidentate (two CH-π) complexes. All model complexes were optimized using the DFT-D approach, at the BP/def2-TZVPP level of theory. The interaction energies were refined using single point calculations at highly correlated ab initio methods at the CCSD(T)/CBS level, calculated as E + (E(CCSD(T))-E(MP2))(Small Basis). Bidentate complexes show very strong interactions in the range from -10.79 up to -7.15 and -8.20 up to -6.14 kcal mol(-1) for the DFT-D and CCSD(T)/CBS level, respectively. These values were compared with the sum of interaction energies of the appropriate monodentate carbohydrate-naphthalene complexes. The comparison reveals that the bidentate complex interaction energy is higher (interaction is weaker) than the sum of monodentate complex interaction energies. Bidentate complex interaction energy corresponds to 2/3 of the sum of the appropriate monodentate complex interaction energies (averaging over all modeled carbohydrate complexes). The observed interaction energies were also compared with the sum of interaction energies of the corresponding previously published carbohydrate-benzene complexes. Also in this case the interaction energy of the bidentate complex was higher (i.e. weaker interaction) than the sum of interaction energies of the corresponding benzene complexes. However, the obtained difference is lower than before, while the bidentate complex interaction energy corresponds to 4/5 of the sum of interaction energy of the benzene complexes, averaged over all structures. The mentioned comparison might aid protein engineering efforts where amino acid residues phenylalanine or tyrosine are to be replaced by a tryptophan and can help to predict the changes in the interactions. The observed results also show that DFT-D correctly describes the CH-π interaction energy and their additive properties in comparison to CCSD(T)/CBS calculated interaction energies. Thus, the DFT-D approach might be used for calculation of larger complexes of biological interest, where dispersion interaction plays an important role.
Collapse
Affiliation(s)
- Stanislav Kozmon
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | | | | | | |
Collapse
|
10
|
Nishio M. The CH/π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates. Phys Chem Chem Phys 2011; 13:13873-900. [PMID: 21611676 DOI: 10.1039/c1cp20404a] [Citation(s) in RCA: 624] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm.
Collapse
Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338 Minamioya, Machida-shi, Tokyo, 194-0031, Japan.
| |
Collapse
|
11
|
Kozmon S, Matuška R, Spiwok V, Koča J. Three-dimensional potential energy surface of selected carbohydrates' CH/π dispersion interactions calculated by high-level quantum mechanical methods. Chemistry 2011; 17:5680-90. [PMID: 21480404 DOI: 10.1002/chem.201002876] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Indexed: 11/10/2022]
Abstract
In this study we present the first systematic computational three-dimensional scan of carbohydrate hydrophobic patches for the ability to interact through CH/π dispersion interactions. The carbohydrates β-d-glucopyranose, β-d-mannopyranose and α-l-fucopyranose were studied in a complex with a benzene molecule, which served as a model of the CH/π interaction in carbohydrate/protein complexes. The 3D relaxed scans were performed at the SCC-DFTB-D level with 3 757 grid points for both carbohydrate hydrophobic sides. The interaction energy of all grid points was recalculated at the DFT-D BP/def2-TZVPP level. The results obtained clearly show highly delimited and separated areas around each CH group, with an interaction energy up to -5.40 kcal mol(-1) . The results also show that with increasing H⋅⋅⋅π distance these delimited areas merge and form one larger region, which covers all hydrogen atoms on that specific carbohydrate side. Simultaneously, the interaction becomes weaker with an energy of -2.5 kcal mol(-1) . All local energy minima were optimized at the DFT-D BP/def2-TZVPP level and the interaction energies of these complexes were refined by use of the high-level ab initio computation at the CCSD(T)/CBS level. Results obtained from the optimization suggest that the CH group hydrogen atoms are not equivalent and the interaction energy at the CCSD(T)/CBS level range from -3.54 to -5.40 kcal mol(-1) . These results also reveal that the optimal H⋅⋅⋅π distance for the CH/π dispersion interaction is approximately (2.310±0.030) Å, and the angle defined as carbon-hydrogen-benzene geometrical centre is (180±30)°. These results reveal that whereas the dispersion interactions with the lowest interaction energies are quite strictly located in space, the slightly higher interaction energy regions adopt a much larger space.
Collapse
Affiliation(s)
- Stanislav Kozmon
- National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | | | | | | |
Collapse
|
12
|
Kumari M, Balaji PV, Sunoj RB. Quantification of binding affinities of essential sugars with a tryptophan analogue and the ubiquitous role of C-H···π interactions. Phys Chem Chem Phys 2011; 13:6517-30. [PMID: 21369604 DOI: 10.1039/c0cp02559c] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of noncovalent interactions in carbohydrate recognition by aromatic amino acids has long been reported. To develop a molecular understanding of noncovalent interactions in the recognition process, we have examined a series of binary complexes between 3-methylindole (3-MeIn) and sugars. In particular, the geometries and binding affinities of 3-MeIn with α/β-D-glucose, β-D-galactose, α-D-mannose and α/β-L-fucose are obtained using the MP2(full)/6-31G(d,p) and the M06/TZV2D//MP2/6-31G(d,p) level of theories. The conventional hydrogen bonding such as N-H···O and C-H···O as well as nonconventional O-H···π and C-H···π type of interactions is, in general, identified as responsible for the moderately strong interaction energies. Large variations in the position-orientations of 3-MeIn with respect to saccharide are noticed, within the same sugar family, as well as across different sugar series. Furthermore, complexes with large differences in their geometries are recognized as capable of exhibiting very similar interaction energies, underscoring the significance of exhaustive conformation sampling, as carried out in the present study. These observations are readily attributed to the differences in the efficiency of the type of interactions enlisted above. The highest and lowest interaction energies, upon inclusion of 50% BSSE correction, are found to be -16.02 and -6.22 kcal mol(-1), respectively, for α-D-glucose (1a) and α-L-fucose (5j). While more number of prominent conventional hydrogen bonding contacts remains as a characteristic feature of the strongly bound complexes, the lower end of the interaction energy spectrum is dominated by multiple C-H···π interactions. The complexes exhibiting as many as four C-H···π contacts are identified in the case of α/β-D-glucose, β-D-galactose, and α/β-L-fucose with an interaction energy hovering around -8 kcal mol(-1). The presence of effective C-H···π interactions is found to be dependent on the saccharide configuration as well as the area of the apolar patch constituted by the C-H groups. The study offers a comprehensive set of binary complexes, across different saccharides, which serves as an illustration of the significance and ubiquitous nature of C-H···π interactions in carbohydrate binding in saccharide-protein complexes.
Collapse
Affiliation(s)
- Manju Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | | |
Collapse
|
13
|
Takahashi O, Kohno Y, Nishio M. Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations. Chem Rev 2011; 110:6049-76. [PMID: 20550180 DOI: 10.1021/cr100072x] [Citation(s) in RCA: 447] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osamu Takahashi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
| | | | | |
Collapse
|
14
|
An evaluation of the GLYCAM06 and MM3 force fields, and the PM3-D* molecular orbital method for modelling prototype carbohydrate–aromatic interactions. J Mol Graph Model 2010; 29:321-5. [DOI: 10.1016/j.jmgm.2010.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 07/09/2010] [Indexed: 11/23/2022]
|
15
|
Ma C, Liang W, Jiang D, Hong Z, Qing L, Yan Y. Theoretical study of the photophysical and charge transport properties of novel fluorescent fluorine–boron compounds. Mol Phys 2010. [DOI: 10.1080/00268971003657102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
16
|
Clayden J, Hennecke U, Vincent MA, Hillier IH, Helliwell M. The origin of the conformational preference of N,N′-diaryl-N,N′-dimethyl ureas. Phys Chem Chem Phys 2010; 12:15056-64. [DOI: 10.1039/c0cp00571a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
17
|
Raju RK, Hillier IH, Burton NA, Vincent MA, Doudou S, Bryce RA. The effects of perfluorination on carbohydrate–π interactions: computational studies of the interaction of benzene and hexafluorobenzene with fucose and cyclodextrin. Phys Chem Chem Phys 2010; 12:7959-67. [DOI: 10.1039/c002058c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
18
|
Nishio M, Umezawa Y, Honda K, Tsuboyama S, Suezawa H. CH/π hydrogen bonds in organic and organometallic chemistry. CrystEngComm 2009. [DOI: 10.1039/b902318f] [Citation(s) in RCA: 481] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
19
|
Raju RK, Ramraj A, Vincent MA, Hillier IH, Burton NA. Carbohydrate-protein recognition probed by density functional theory and ab initio calculations including dispersive interactions. Phys Chem Chem Phys 2008; 10:6500-8. [PMID: 18979035 DOI: 10.1039/b809164a] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Carbohydrate-protein recognition has been studied by electronic structure calculations of complexes of fucose and glucose with toluene, p-hydroxytoluene and 3-methylindole, the latter aromatic molecules being analogues of phenylalanine, tyrosine and tryptophan, respectively. We use mainly a density functional theory model with empirical corrections for the dispersion interactions (DFT-D), this method being validated by comparison with a limited number of high level ab initio calculations. We have calculated both binding energies of the complexes as well as their harmonic vibrational frequencies and proton NMR chemical shifts. We find a range of minimum energy structures in which the aromatic group can bind to either of the two faces of the carbohydrate, the binding being dominated by a combination of OH-pi and CH-pi dispersive interactions. For the fucose-toluene and alpha-methyl glucose-toluene complexes, the most stable structures involve OH-pi interactions, which are reflected in a red shift of the corresponding O-H stretching frequency, in good quantitative agreement with experimental data. For those structures where CH-pi interactions are found we predict a corresponding blue shift in the C-H frequency, which parallels the predicted proton NMR shift. We find that the interactions involving 3-methylindole are somewhat greater than those for toluene and p-hydroxytoluene.
Collapse
Affiliation(s)
- Rajesh K Raju
- School of Chemistry, University of Manchester, Oxford Road, Manchester, UKM13 9PL
| | | | | | | | | |
Collapse
|