1
|
Pinillos P, Camiruaga A, Torres-Hernández F, Basterrechea FJ, Usabiaga I, Fernández JA. Exploring the interaction sites in glucose and galactose using phenol as a probe. Phys Chem Chem Phys 2023; 25:7205-7212. [PMID: 36846922 DOI: 10.1039/d2cp06036a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Sugars, together with amino acids and nucleobases, are the fundamental building blocks of a cell. They are involved in many fundamental processes and they especially play relevant roles as part of the immune system. The latter is connected to their ability to establish a collection of intermolecular interactions, depending on the position of their hydroxyl groups. Here we explore how the position of the OH in C4, the anomeric conformation and the nature substituent affect the interaction with phenol, which serves as a probe of the preferred site for the interaction. Using mass-resolved excitation spectroscopy and density functional calculations, we unravel the structure of the dimers and compare their conformation with those found for similar systems. The main conclusion is that the hydroxymethyl group has a very strong influence, guiding the whole aggregation process and that the position of the substituent in C4 has a stronger influence on the final structure of the dimer than the anomeric conformation.
Collapse
Affiliation(s)
- Paúl Pinillos
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Ander Camiruaga
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Fernando Torres-Hernández
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Francisco J Basterrechea
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Imanol Usabiaga
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - José A Fernández
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| |
Collapse
|
2
|
The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases. Nat Commun 2022; 13:5577. [PMID: 36151080 PMCID: PMC9508125 DOI: 10.1038/s41467-022-33180-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/03/2022] [Indexed: 11/08/2022] Open
Abstract
In the barley β-D-glucan glucohydrolase, a glycoside hydrolase family 3 (GH3) enzyme, the Trp286/Trp434 clamp ensures β-D-glucosides binding, which is fundamental for substrate hydrolysis during plant growth and development. We employ mutagenesis, high-resolution X-ray crystallography, and multi-scale molecular modelling methods to examine the binding and conformational behaviour of isomeric β-D-glucosides during substrate-product assisted processive catalysis that operates in GH3 hydrolases. Enzyme kinetics reveals that the W434H mutant retains broad specificity, while W434A behaves as a strict (1,3)-β-D-glucosidase. Investigations of reactant movements on the nanoscale reveal that processivity is sensitive to mutation-specific alterations of the tryptophan clamp. While wild-type and W434H utilise a lateral cavity for glucose displacement and sliding of (1,3)-linked hydrolytic products through the catalytic site without dissociation, consistent with their high hydrolytic rates, W434A does not adopt processive catalysis. Phylogenomic analyses of GH3 hydrolases disclose the evolutionary advantage of the tryptophan clamp that confers broad specificity, high catalytic efficiency, and processivity.
Collapse
|
3
|
Site-selective, stereocontrolled glycosylation of minimally protected sugars. Nature 2022; 608:74-79. [PMID: 35709829 PMCID: PMC9427130 DOI: 10.1038/s41586-022-04958-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 11/08/2022]
Abstract
The identification of general and efficient methods for the construction of oligosaccharides stands as one of the great challenges for the field of synthetic chemistry1,2. Selective glycosylation of unprotected sugars and other polyhydroxylated nucleophiles is a particularly significant goal, requiring not only control over the stereochemistry of the forming bond but also differentiation between similarly reactive nucleophilic sites in stereochemically complex contexts3,4. Chemists have generally relied on multi-step protecting-group strategies to achieve site control in glycosylations, but practical inefficiencies arise directly from the application of such approaches5-7. We describe here a new strategy for small-molecule-catalyst-controlled, highly stereo- and site-selective glycosylations of unprotected or minimally protected mono- and disaccharides using precisely designed bis-thiourea small-molecule catalysts. Stereo- and site-selective galactosylations and mannosylations of a wide assortment of polyfunctional nucleophiles is thereby achieved. Kinetic and computational studies provide evidence that site selectivity arises from stabilizing C-H/π interactions between the catalyst and the nucleophile, analogous to those documented in sugar-binding proteins. This work demonstrates that highly selective glycosylation reactions can be achieved through control of stabilizing noncovalent interactions, a potentially general strategy for selective functionalization of carbohydrates.
Collapse
|
4
|
Kapros A, Balázs A, Harmat V, Háló A, Budai L, Pintér I, Menyhárd DK, Perczel A. Configuration-Controlled Crystal and/or Gel Formation of Protected d-Glucosamines Supported by Promiscuous Interaction Surfaces and a Conformationally Heterogeneous Solution State. Chemistry 2020; 26:11643-11655. [PMID: 32333713 DOI: 10.1002/chem.202000882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/17/2020] [Indexed: 11/10/2022]
Abstract
The configuration-dependent self-association mode of the two anomers of O-Ac,N-Fmoc-d-glucosamine, a foldamer building block, leading to gel and/or single crystal formation is described. The β-anomer of the sugar amino acid (2) forms a gel from various solvents (confirmed by SEM, rheology measurements, NMR, and ECD spectroscopy), whereas the α-anomer (1) does not form a gel with any solvent tested. Transition from the solution state to a gel is coupled to a concurrent shift of the Fmoc-groups: from a freely rotating (almost symmetrical) to a specific, asymmetric orientation. Whereas the crystal structure of the α-anomer is built as an evenly packed 3D system, the β-anomer forms a looser superstructure of well-packed 2D layers. Modeling indicates that in the lowest energy, but scarcely sampled conformer of the β-anomer, the Fmoc-group bends above the sugar moiety, stabilized by intramolecular CH↔π interactions between the aromatic rings. It is concluded that possessing an extended and promiscuous interaction surface and a conformationally heterogeneous solution state are among the basic requirements of gel formation for a candidate molecule.
Collapse
Affiliation(s)
- Anita Kapros
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - Attila Balázs
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - Veronika Harmat
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary.,MTA-ELTE Protein Modelling Research Group, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - Adrienn Háló
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - Lívia Budai
- Department of Pharmaceutics, Semmelweis University, Hőgyes Endre utca 7, Budapest, 1092, Hungary
| | - István Pintér
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - Dóra K Menyhárd
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary.,MTA-ELTE Protein Modelling Research Group, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary.,MTA-ELTE Protein Modelling Research Group, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| |
Collapse
|
5
|
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
|
6
|
Fujdiarová E, Houser J, Dobeš P, Paulíková G, Kondakov N, Kononov L, Hyršl P, Wimmerová M. Heptabladed β‐propeller lectins PLL2 and PHL from
Photorhabdus
spp. recognize
O
‐methylated sugars and influence the host immune system. FEBS J 2020; 288:1343-1365. [DOI: 10.1111/febs.15457] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 04/19/2020] [Accepted: 06/15/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Eva Fujdiarová
- Central European Institute of Technology (CEITEC) Masaryk University Brno Czech Republic
- National Centre for Biomolecular Research Faculty of Science Masaryk University Brno Czech Republic
| | - Josef Houser
- Central European Institute of Technology (CEITEC) Masaryk University Brno Czech Republic
- National Centre for Biomolecular Research Faculty of Science Masaryk University Brno Czech Republic
| | - Pavel Dobeš
- National Centre for Biomolecular Research Faculty of Science Masaryk University Brno Czech Republic
- Section of Animal Physiology and Immunology Department of Experimental Biology Faculty of Science Masaryk University Brno Czech Republic
| | - Gita Paulíková
- Central European Institute of Technology (CEITEC) Masaryk University Brno Czech Republic
- National Centre for Biomolecular Research Faculty of Science Masaryk University Brno Czech Republic
| | - Nikolay Kondakov
- N.D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences Moscow Russia
| | - Leonid Kononov
- N.D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences Moscow Russia
| | - Pavel Hyršl
- Section of Animal Physiology and Immunology Department of Experimental Biology Faculty of Science Masaryk University Brno Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology (CEITEC) Masaryk University Brno Czech Republic
- National Centre for Biomolecular Research Faculty of Science Masaryk University Brno Czech Republic
- Department of Biochemistry Faculty of Science Masaryk University Brno Czech Republic
| |
Collapse
|
7
|
Wang Y, Wang Z, Wang S, Chen Z, Chen J, Chen Y, Fu J. Magnetic poly(cyclotriphosphazene-co-4,4′-sulfonyldiphenol) nanotubes modified with glacial acetic acid for removing methylene blue: Adsorption performance and mechanism. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.08.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
8
|
Samie A, Salimi A, Garrison JC. Exploration of relative π-electron localization in naphthalene aromatic rings by C–H⋯π interactions: experimental evidence, computational criteria, and database analysis. CrystEngComm 2019. [DOI: 10.1039/c9ce00929a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In C–H⋯π interaction, the relative π-electron localization in aromatic ring led to the change of contact position from centre to edges of the ring (C–H⋯πe) which was confirmed by experimental evidences, computational criteria, and database analysis.
Collapse
Affiliation(s)
- Ali Samie
- Department of Chemistry
- Faculty of Science
- Ferdowsi University of Mashhad
- Mashhad
- Iran
| | - Alireza Salimi
- Department of Chemistry
- Faculty of Science
- Ferdowsi University of Mashhad
- Mashhad
- Iran
| | - Jered C. Garrison
- Department of Pharmaceutical Sciences
- University of Nebraska Medical Centre
- USA
| |
Collapse
|
9
|
Schiefner A, Angelov A, Liebl W, Skerra A. Structural basis for cellulose binding by the type A carbohydrate-binding module 64 of Spirochaeta thermophila. Proteins 2016; 84:855-8. [PMID: 26868291 DOI: 10.1002/prot.25010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 01/04/2016] [Accepted: 01/25/2016] [Indexed: 11/06/2022]
Abstract
Spirochaeta thermophila secretes seven glycoside hydrolases for plant biomass degradation that carry a carbohydrate-binding module 64 (CBM64) appended at the C-terminus. CBM64 adsorbs to various β1-4-linked pyranose substrates and shows high affinity for cellulose. We present the first crystal structure of a CBM64 at 1.2 Å resolution, which reveals a jelly-roll-like fold corresponding to a surface-binding type A CBM. Modeling of its interaction with cellulose indicates that CBM64 achieves association with the hydrophobic face of β-linked pyranose chains via a unique coplanar arrangement of four exposed tryptophan side chains. Proteins 2016; 84:855-858. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- André Schiefner
- Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising (Weihenstephan), Germany
| | - Angel Angelov
- Lehrstuhl Für Mikrobiologie, Technische Universität München, 85354 Freising (Weihenstephan), Germany
| | - Wolfgang Liebl
- Lehrstuhl Für Mikrobiologie, Technische Universität München, 85354 Freising (Weihenstephan), Germany
| | - Arne Skerra
- Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising (Weihenstephan), Germany
| |
Collapse
|
10
|
Cui X, Cai W, Shao X. Glucose induced variation of water structure from temperature dependent near infrared spectra. RSC Adv 2016. [DOI: 10.1039/c6ra18912a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The different effects of glucose on water species provide evidence to explain the bioprotective function of carbohydrates in aqueous solutions.
Collapse
Affiliation(s)
- Xiaoyu Cui
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | - Wensheng Cai
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | - Xueguang Shao
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| |
Collapse
|
11
|
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
|
12
|
Molecular simulations of hevein/(GlcNAc)3 complex with weakened OH/O and CH/π hydrogen bonds: implications for their role in complex stabilization. Carbohydr Res 2015; 408:1-7. [PMID: 25816996 DOI: 10.1016/j.carres.2015.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 11/23/2022]
Abstract
Carbohydrate-protein complexes are often characterized by interactions via aromatic amino acid residues. Several mechanisms have been proposed to explain these stacking-like interactions between pyranose sugars and aromatic moieties. The physical basis of these interactions is being explained as either dispersion CH/π or hydrophobic. In order to elucidate the nature of these interactions, we performed a series of molecular dynamics simulation of hevein domain (HEV32) in complex with (β-D-GlcNAc)3. Selected OH/O and CH/π hydrogen bonds involved in carbohydrate recognition were artificially weakened in 100 ns molecular dynamics simulations. Separate weakening of either OH/O or CH/π hydrogen bonds was not sufficient to destabilize the complex. This indicates that other effects, not solely CH/π dispersion interactions, contribute significantly to the stability of the complex. Significant destabilization of complexes was reached only by simultaneous weakening of OH/O and CH/π hydrogen bonds. This also shows that classical hydrogen bonds and CH/π interactions are working in concert to stabilize this carbohydrate-protein test case.
Collapse
|
13
|
Wilson KA, Wetmore SD. A Survey of DNA–Protein π–Interactions: A Comparison of Natural Occurrences and Structures, and Computationally Predicted Structures and Strengths. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
14
|
Govender KK, Naidoo KJ. Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations. J Chem Theory Comput 2014; 10:4708-17. [DOI: 10.1021/ct500373p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Krishna K. Govender
- Scientific Computing
Research Unit and Department
of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kevin J. Naidoo
- Scientific Computing
Research Unit and Department
of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| |
Collapse
|
15
|
Wheeler SE, Bloom JWG. Toward a more complete understanding of noncovalent interactions involving aromatic rings. J Phys Chem A 2014; 118:6133-47. [PMID: 24937084 DOI: 10.1021/jp504415p] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Noncovalent interactions involving aromatic rings, which include π-stacking interactions, anion-π interactions, and XH-π interactions, among others, are ubiquitous in chemical and biochemical systems. Despite dramatic advances in our understanding of these interactions over the past decade, many aspects of these noncovalent interactions have only recently been uncovered, with many questions remaining. We summarize our computational studies aimed at understanding the impact of substituents and heteroatoms on these noncovalent interactions. In particular, we discuss our local, direct interaction model of substituent effects in π-stacking interactions. In this model, substituent effects are dominated by electrostatic interactions of the local dipoles associated with the substituents and the electric field of the other ring. The implications of the local nature of substituent effects on π-stacking interactions in larger systems are discussed, with examples given for complexes with carbon nanotubes and a small graphene model, as well as model stacked discotic systems. We also discuss related issues involving the interpretation of electrostatic potential (ESP) maps. Although ESP maps are widely used in discussions of noncovalent interactions, they are often misinterpreted. Next, we provide an alternative explanation for the origin of anion-π interactions involving substituted benzenes and N-heterocycles, and show that these interactions are well-described by simple models based solely on charge-dipole interactions. Finally, we summarize our recent work on the physical nature of substituent effects in XH-π interactions. Together, these results paint a more complete picture of noncovalent interactions involving aromatic rings and provide a firm conceptual foundation for the rational exploitation of these interactions in a myriad of chemical contexts.
Collapse
Affiliation(s)
- Steven E Wheeler
- Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
| | | |
Collapse
|
16
|
Wilson KA, Kellie JL, Wetmore SD. DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar. Nucleic Acids Res 2014; 42:6726-41. [PMID: 24744240 PMCID: PMC4041443 DOI: 10.1093/nar/gku269] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π-π stacking, π-π T-shaped or sugar-π contacts. Three hundred forty-four nucleobase-amino acid π-π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA-protein sugar-π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C-H···π and/or lone-pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π-π and sugar-π interactions display a range of relative monomer orientations and therefore interaction energies (up to -50 (-70) kJ mol(-1) for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA-protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered.
Collapse
Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| | - Jennifer L Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| |
Collapse
|
17
|
Abstract
The present review summarizes recently developed calixarene derivatives for protein surface recognition which are able to identify, inhibit, and separate specific proteins.
Collapse
Affiliation(s)
- Reza Zadmard
- Chemistry and Chemical Engineering
- Research Center of Iran
- , Iran
| | | |
Collapse
|
18
|
Chen W, Enck S, Price JL, Powers DL, Powers ET, Wong CH, Dyson HJ, Kelly JW. Structural and energetic basis of carbohydrate-aromatic packing interactions in proteins. J Am Chem Soc 2013; 135:9877-84. [PMID: 23742246 DOI: 10.1021/ja4040472] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Carbohydrate-aromatic interactions mediate many biological processes. However, the structure-energy relationships underpinning direct carbohydrate-aromatic packing interactions in aqueous solution have been difficult to assess experimentally and remain elusive. Here, we determine the structures and folding energetics of chemically synthesized glycoproteins to quantify the contributions of the hydrophobic effect and CH-π interactions to carbohydrate-aromatic packing interactions in proteins. We find that the hydrophobic effect contributes significantly to protein-carbohydrate interactions. Interactions between carbohydrates and aromatic amino acid side chains, however, are supplemented by CH-π interactions. The strengths of experimentally determined carbohydrate CH-π interactions do not correlate with the electrostatic properties of the involved aromatic residues, suggesting that the electrostatic component of CH-π interactions in aqueous solution is small. Thus, tight binding of carbohydrates and aromatic residues is driven by the hydrophobic effect and CH-π interactions featuring a dominating dispersive component.
Collapse
Affiliation(s)
- Wentao Chen
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Mitchell FL, Neres J, Ramraj A, Raju RK, Hillier IH, Vincent MA, Bryce RA. Insights into the activity and specificity of Trypanosoma cruzi trans-sialidase from molecular dynamics simulations. Biochemistry 2013; 52:3740-51. [PMID: 23672572 PMCID: PMC3675669 DOI: 10.1021/bi301112p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
![]()
Trypanosoma cruzitrans-sialidase
(TcTS), which catalyzes the transfer or hydrolysis of terminal sialic
acid residues, is crucial to the development and proliferation of
the T. cruzi parasite and thus has emerged as a potential
drug target for the treatment of Chagas disease. We here probe the
origin of the observed preference for the transfer reaction over hydrolysis
where the substrate for TcTS is the natural sialyl donor (represented
in this work by sialyllactose). Thus, acceptor lactose preferentially
attacks the sialyl-enyzme intermediate rather than water. We compare
this with the weaker preference for such transfer shown by a synthetic
donor substrate, 4-methylumbelliferyl α-d-acetylneuraminide.
For this reason, we conducted molecular dynamics simulations of TcTS
following its sialylation by the substrate to examine the behavior
of the asialyl leaving group by the protein. These simulations indicate
that, where lactose is released, this leaving group samples well-defined
interactions in the acceptor site, some of which are mediated by localized
water molecules; also, the extent of the opening of the acceptor site
to solvent is reduced as compared with those of unliganded forms of
TcTS. However, where there is release of 4-methylumbelliferone, this
leaving group explores a range of transient poses; surrounding active
site water is also more disordered. The acceptor site explores more
open conformations, similar to the case in which the 4-methylumbelliferone
is absent. Thus, the predicted solvent accessibility of sialylated
TcTS is increased when 4-methylumbelliferyl α-d-acetylneuraminide
is the substrate compared to sialyllactose; this in turn is likely
to contribute to a greater propensity for hydrolysis of the covalent
intermediate. These computational simulations, which suggest that
protein flexibility has a role in the transferase/sialidase activity
of TcTS, have the potential to aid in the design of anti-Chagas inhibitors
effective against this neglected tropical disease.
Collapse
Affiliation(s)
- Felicity L Mitchell
- School of Pharmacy and Pharmaceutical Sciences and ‡School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PT, U.K
| | | | | | | | | | | | | |
Collapse
|
20
|
Toukach FV, Ananikov VP. Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations. Chem Soc Rev 2013; 42:8376-415. [DOI: 10.1039/c3cs60073d] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
21
|
Stacking interactions between carbohydrate and protein quantified by combination of theoretical and experimental methods. PLoS One 2012; 7:e46032. [PMID: 23056230 PMCID: PMC3466270 DOI: 10.1371/journal.pone.0046032] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 08/28/2012] [Indexed: 11/21/2022] Open
Abstract
Carbohydrate – receptor interactions are an integral part of biological events. They play an important role in many cellular processes, such as cell-cell adhesion, cell differentiation and in-cell signaling. Carbohydrates can interact with a receptor by using several types of intermolecular interactions. One of the most important is the interaction of a carbohydrate's apolar part with aromatic amino acid residues, known as dispersion interaction or CH/π interaction. In the study presented here, we attempted for the first time to quantify how the CH/π interaction contributes to a more general carbohydrate - protein interaction. We used a combined experimental approach, creating single and double point mutants with high level computational methods, and applied both to Ralstonia solanacearum (RSL) lectin complexes with α-l-Me-fucoside. Experimentally measured binding affinities were compared with computed carbohydrate-aromatic amino acid residue interaction energies. Experimental binding affinities for the RSL wild type, phenylalanine and alanine mutants were −8.5, −7.1 and −4.1 kcal.mol−1, respectively. These affinities agree with the computed dispersion interaction energy between carbohydrate and aromatic amino acid residues for RSL wild type and phenylalanine, with values −8.8, −7.9 kcal.mol−1, excluding the alanine mutant where the interaction energy was −0.9 kcal.mol−1. Molecular dynamics simulations show that discrepancy can be caused by creation of a new hydrogen bond between the α-l-Me-fucoside and RSL. Observed results suggest that in this and similar cases the carbohydrate-receptor interaction can be driven mainly by a dispersion interaction.
Collapse
|
22
|
In search of OH–π interactions between 1-methylimidazole and water using a combined computational quantum chemistry and ATR-FTIR spectroscopy approach. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
23
|
Bloom JWG, Raju RK, Wheeler SE. Physical Nature of Substituent Effects in XH/π Interactions. J Chem Theory Comput 2012; 8:3167-74. [DOI: 10.1021/ct300520n] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jacob W. G. Bloom
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Rajesh K. Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
24
|
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]
|
25
|
Raju RK, Bloom JWG, An Y, Wheeler SE. Substituent effects on non-covalent interactions with aromatic rings: insights from computational chemistry. Chemphyschem 2011; 12:3116-30. [PMID: 21928437 DOI: 10.1002/cphc.201100542] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Indexed: 02/01/2023]
Abstract
Non-covalent interactions with aromatic rings pervade modern chemical research. The strength and orientation of these interactions can be tuned and controlled through substituent effects. Computational studies of model complexes have provided a detailed understanding of the origin and nature of these substituent effects, and pinpointed flaws in entrenched models of these interactions in the literature. Here, we provide a brief review of efforts over the last decade to unravel the origin of substituent effects in π-stacking, XH/π, and ion/π interactions through detailed computational studies. We highlight recent progress that has been made, while also uncovering areas where future studies are warranted.
Collapse
Affiliation(s)
- Rajesh K Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, USA
| | | | | | | |
Collapse
|
26
|
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
|
27
|
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
|
28
|
Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
29
|
Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1167] [Impact Index Per Article: 89.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
Collapse
Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
| | | | | |
Collapse
|
30
|
Roldós V, Cañada FJ, Jiménez-Barbero J. Carbohydrate-Protein Interactions: A 3D View by NMR. Chembiochem 2011; 12:990-1005. [DOI: 10.1002/cbic.201000705] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Indexed: 12/29/2022]
|
31
|
Cocinero EJ, Çarçabal P, Vaden TD, Davis BG, Simons JP. Exploring Carbohydrate−Peptide Interactions in the Gas Phase: Structure and Selectivity in Complexes of Pyranosides with N-Acetylphenylalanine Methylamide. J Am Chem Soc 2011; 133:4548-57. [DOI: 10.1021/ja109664k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emilio J. Cocinero
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Pierre Çarçabal
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Timothy D. Vaden
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Benjamin G. Davis
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - John P. Simons
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| |
Collapse
|
32
|
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
|
33
|
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
|
34
|
Vincent MA, Hillier IH. The structure and interaction energies of the weak complexes of CHClF2 and CHF3 with HCCH: a test of density functional theory methods. Phys Chem Chem Phys 2011; 13:4388-92. [DOI: 10.1039/c0cp02626c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
35
|
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]
|
36
|
Taylor CJ, Nix MGD, Dessent CEH. Noncovalent Interactions in the Gas-Phase Conformers of Anionic Iduronate (methyl 2-O-sulfo-α-L-iduronate): Variation of Subconformer versus Ring Conformer Energetics for a Prototypical Anionic Monosaccharide Studied Using Computational Methods. J Phys Chem A 2010; 114:11153-60. [DOI: 10.1021/jp102657t] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
| | - Michael G. D. Nix
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
| | | |
Collapse
|
37
|
Mitchell FL, Miles SM, Neres J, Bichenkova EV, Bryce RA. Tryptophan as a molecular shovel in the glycosyl transfer activity of Trypanosoma cruzi trans-sialidase. Biophys J 2010; 98:L38-40. [PMID: 20441732 DOI: 10.1016/j.bpj.2010.01.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 01/05/2010] [Accepted: 01/13/2010] [Indexed: 10/19/2022] Open
Abstract
Molecular dynamics investigations into active site plasticity of Trypanosoma cruzi trans-sialidase, a protein implicated in Chagas disease, suggest that movement of the Trp(312) loop plays an important role in the enzyme's sialic acid transfer mechanism. The observed Trp(312) flexibility equates to a molecular shovel action, which leads to the expulsion of the donor aglycone leaving group from the catalytic site. These computational simulations provide detailed structural insights into sialyl transfer by the trans-sialidase and may aid the design of inhibitors effective against this neglected tropical disease.
Collapse
Affiliation(s)
- Felicity L Mitchell
- School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester, United Kingdom
| | | | | | | | | |
Collapse
|
38
|
Ramírez-Gualito K, Alonso-Ríos R, Quiroz-García B, Rojas-Aguilar A, Díaz D, Jiménez-Barbero J, Cuevas G. Enthalpic nature of the CH/pi interaction involved in the recognition of carbohydrates by aromatic compounds, confirmed by a novel interplay of NMR, calorimetry, and theoretical calculations. J Am Chem Soc 2010; 131:18129-38. [PMID: 19928848 DOI: 10.1021/ja903950t] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Specific interactions between molecules, including those produced by a given solute, and the surrounding solvent are essential to drive molecular recognition processes. A simple molecule such as benzene is capable of recognizing and differentiating among very similar entities, such as methyl 2,3,4,6-tetra-O-methyl-alpha-D-galactopyranoside (alpha-Me(5)Gal), methyl 2,3,4,6-tetra-O-methyl-beta-D-galactopyranoside (beta-Me(5)Gal), 1,2,3,4,6-penta-O-acetyl-beta-D-galactopyranose (beta-Ac(5)Gal), and methyl 2,3,4,6-tetra-O-methyl-alpha-D-mannopyranoside (alpha-Me(5)Man). In order to determine if these complexes are formed, the interaction energy between benzene and the different carbohydrates was determined, using Calvet microcalorimetry, as the enthalpy of solvation. These enthalpy values were -89.0 +/- 2.0, -88.7 +/- 5.5, -132.5 +/- 6.2, and -78.8 +/- 3.9 kJ mol(-1) for the four complexes, respectively. Characterization of the different complexes was completed by establishing the molecular region where the interaction takes place using NMR. It was determined that beta-Me(5)Gal is stabilized by the CH/pi interaction produced by the nonpolar region of the carbohydrate on the alpha face. In contrast, alpha-Me(5)Man is not specifically solvated by benzene and does not present any stacking interaction. Although alpha-Me(5)Gal has a geometry similar to that of its epimer, the obtained NMR data seem to indicate that the axial methoxy group at the anomeric position increases the distance of the benzene molecules from the pyranose ring. Substitution of the methoxy groups by acetate moieties, as in beta-Ac(5)Gal, precludes the approach of benzene to produce the CH/pi interaction. In fact, the elevated stabilization energy of beta-Ac(5)Gal is probably due to the interaction between benzene and the methyl groups of the acetyls. Therefore, methoxy and acetyl substituents have different effects on the protons of the pyranose ring.
Collapse
Affiliation(s)
- Karla Ramírez-Gualito
- Instituto de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70213, 04510 Coyoacán, Circuito Exterior, México D.F., México.
| | | | | | | | | | | | | |
Collapse
|
39
|
Mazik M, Hartmann A. Recognition properties of receptors consisting of imidazole and indole recognition units towards carbohydrates. Beilstein J Org Chem 2010; 6:9. [PMID: 20485591 PMCID: PMC2871371 DOI: 10.3762/bjoc.6.9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 01/19/2010] [Indexed: 11/25/2022] Open
Abstract
Compounds 4 and 5, including both 4(5)-substituted imidazole or 3-substituted indole units as the entities used in nature, and 2-aminopyridine group as a heterocyclic analogue of the asparagine/glutamine primary amide side chain, were prepared and their binding properties towards carbohydrates were studied. The design of these receptors was inspired by the binding motifs observed in the crystal structures of protein-carbohydrate complexes. ¹H NMR spectroscopic titrations in competitive and non-competitive media as well as binding studies in two-phase systems, such as dissolution of solid carbohydrates in apolar media, revealed both highly effective recognition of neutral carbohydrates and interesting binding preferences of these acyclic compounds. Compared to the previously described acyclic receptors, compounds 4 and 5 showed significantly increased binding affinity towards β-galactoside. Both receptors display high β- vs. α-anomer binding preferences in the recognition of glycosides. It has been shown that both hydrogen bonding and interactions of the carbohydrate CH units with the aromatic rings of the receptors contribute to the stabilization of the receptor-carbohydrate complexes. The molecular modeling calculations, synthesis and binding properties of 4 and 5 towards selected carbohydrates are described and compared with those of the previously described receptors.
Collapse
Affiliation(s)
- Monika Mazik
- Institut für Organische Chemie der Technischen Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.
| | | |
Collapse
|
40
|
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]
|
41
|
Cocinero E, Stanca-Kaposta E, Dethlefsen M, Liu B, Gamblin D, Davis B, Simons J. Hydration of Sugars in the Gas Phase: Regioselectivity and Conformational Choice inN-Acetyl Glucosamine and Glucose. Chemistry 2009; 15:13427-34. [DOI: 10.1002/chem.200901830] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
42
|
Raju RK, Ramraj A, Hillier IH, Vincent MA, Burton NA. Carbohydrate-aromatic pi interactions: a test of density functionals and the DFT-D method. Phys Chem Chem Phys 2009; 11:3411-6. [PMID: 19421542 DOI: 10.1039/b822877a] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The performance of a number of computational approaches based upon density functional theory (DFT) for the accurate description of carbohydrate-pi interactions is described. A database containing interaction energies of a small number of representative complexes, computed at a high ab initio level, is described, and is used to judge 18 different density functionals including the M05 and M06 families as well as the DFT method augmented with empirical dispersive corrections (DFT-D). The DFT-D method and the M06 functionals are found to perform particularly well, whilst traditional functionals such as B3LYP perform poorly. The interaction energies for 23 sugar-aromatic complexes calculated by the DFT-D method are compared with the values from the 18 functionals. Again, the M06 class of functional is found to be superior.
Collapse
Affiliation(s)
- Rajesh K Raju
- School of Chemistry, University of Manchester, Oxford Road, M13 9PL, Manchester, UK
| | | | | | | | | |
Collapse
|
43
|
Su Z, Cocinero EJ, Stanca-Kaposta EC, Davis BG, Simons JP. Carbohydrate–aromatic interactions: A computational and IR spectroscopic investigation of the complex, methyl α-l-fucopyranoside·toluene, isolated in the gas phase. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.02.043] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
44
|
Anderl T, Audouard C, Miah A, Percy JM, Rinaudo G, Singh K. Syntheses of difluorinated carbasugar phosphates from trifluoroethanol. Org Biomol Chem 2009; 7:5200-6. [DOI: 10.1039/b914068a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
45
|
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]
|