Cation−π Interaction: Its Role and Relevance in Chemistry, Biology, and Material Science

Mahadevi, A. Subha; Sastry, G. Narahari

doi:10.1021/cr300222d

Cited by 967 publications

(790 citation statements)

References 740 publications

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“…5A). The most unique feature of this c-di-GMP binding mode is the extensive guanine-guanine -or arginineguanine cation-stack (55,56), with two guanine bases involved in each stack. The Arg residue again uses its guanidinium group to stack with the guanine base.…”

Section: C-di-gmp At Protein-protein Interfacesmentioning

confidence: 99%

“…It exhibits both H bonding and stacking capability to interact with a guanine base in diverse ways. For example, the guanidinium group can form two bonds to the O-6 and N-7 atoms of a guanine base, by using either its NH1 or NH2 amino group or the N-ε atom, and also stack with a guanine base through the well-known cation-interaction (55,56). In addition, its linear alkyl chain can partially stack upon an aromatic group, enabling it to connect two structural moieties (Fig.…”

Section: C-di-gmp-binding Sites: Why An Arg Residue?mentioning

confidence: 99%

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Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms

2016

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Cyclic di-GMP (c-di-GMP) synthetases and hydrolases (GGDEF, EAL, and HD-GYP domains) can be readily identified in bacterial genome sequences by using standard bioinformatic tools. In contrast, identification of c-di-GMP receptors remains a difficult task, and the current list of experimentally characterized c-di-GMP-binding proteins is likely incomplete. Several classes of c-di-GMP-binding proteins have been structurally characterized; for some others, the binding sites have been identified; and for several potential c-di-GMP receptors, the binding sites remain to be determined. We present here a comparative structural analysis of c-di-GMP-protein complexes that aims to discern the common themes in the binding mechanisms that allow c-di-GMP receptors to bind it with (sub)micromolar affinities despite the 1,000-fold excess of GTP. The available structures show that most receptors use their Arg and Asp/Glu residues to bind c-di-GMP monomers, dimers, or tetramers with stacked guanine bases. The only exception is the EAL domains that bind c-di-GMP monomers in an extended conformation. We show that in c-di-GMPbinding signature motifs, Arg residues bind to the O-6 and N-7 atoms at the Hoogsteen edge of the guanine base, while Asp/Glu residues bind the N-1 and N-2 atoms at its Watson-Crick edge. In addition, Arg residues participate in stacking interactions with the guanine bases of c-di-GMP and the aromatic rings of Tyr and Phe residues. This may account for the presence of Arg residues in the active sites of every receptor protein that binds stacked c-di-GMP. We also discuss the implications of these structural data for the improved understanding of the c-di-GMP signaling mechanisms.

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Section: C-di-gmp At Protein-protein Interfacesmentioning

confidence: 99%

Section: C-di-gmp-binding Sites: Why An Arg Residue?mentioning

confidence: 99%

Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms

2016

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“…27,31,34 Model distances between the C atom in the guanidinium group of R208 and the geometric center of the indole ring of W211 in WT and mutant G ia1 protein models were measured for all conformations [ Fig. 4(C)].…”

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confidence: 99%

Contribution of each Trp residue toward the intrinsic fluorescence of the G_iα1 protein

et al. 2014

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G ia1 is the inhibitory G-protein that, upon activation, reduces the activity of adenylyl cyclase. Comparison of the crystal structures of G ia1 bound to GDP•AMF or GTPcS with that of the inactive, GPD-bound protein indicates that a conformational change occurs in the activation step centered on three switch regions. The contribution of each tryptophan residue (W211 in the switch II region, W131 in the a-helical domain, and W258 in the GTPase domain) toward the intrinsic protein fluorescence was evaluated by using W211F, W131F, and W258F mutants. All three tryptophan residues contributed significantly toward the emission spectra regardless of the conformation. When activated by either GDP•AMF or GTPcS, the observed maximal-fluorescence scaled according to the solvent accessibilities of the tryptophan residues, calculated from molecular dynamics simulations. In the GDP•AMF and GTPcS, but not in the GDP, conformations, the residues W211 and R208 are in close proximity and form a p-cation interaction that results in a red shift in the emission spectra of WT, and W131F and W258F mutants, but a blue shift for the W211F mutant. The observed shifts did not show a relationship with the span of the W211-R208 bridge, but rather with changes in the total interaction energies. Trypsin digestion of the active conformations only occurred for the W211F mutant indicating that the electrostatic p-cation interaction blocks access to R208, which was consistent with the molecular dynamics simulations. We conclude that solvent accessibility and interaction energies account for the fluorescence features of G ia1 .

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“…The hydrogen [1,2], halogen [3][4][5][6][7][8][9][10], chalcogen [11][12][13][14][15][16][17][18][19][20][21][22][23][24], pnictogen [25][26][27][28][29][30][31], tetrel [32] bonding, stacking [33][34][35][36][37], cation/anion-π [38][39][40][41][42], and metallophilic interactions [43][44][45] play key roles in many chemical, physical, and biochemical processes, due to their ability to control structures and properties of associates and supramolecular systems.…”

Section: Introductionmentioning

confidence: 99%

Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes

et al. 2018

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The coupling of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbene)PdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF) suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB). The obtained data indicate the presence of intramolecular S•••Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S•••π in 3a,b, S•••S in 3c, and S•••O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole) does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D) polymeric chains (for 3a,b), dimeric associates (for 3c), or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d) in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a–d: S•••π (3a: 2.4%; 3b: 2.4%), S•••S (3c: less 1%), S•••O (3d: less 1%). The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method), confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry). The AIM analysis demonstrates the presence of appropriate bond critical points for these interactions and defines their strength from 0.9 to 2.8 kcal/mol indicating their attractive nature.

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Cation−π Interaction: Its Role and Relevance in Chemistry, Biology, and Material Science

Cited by 967 publications

References 740 publications

Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms

Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms

Contribution of each Trp residue toward the intrinsic fluorescence of the G_iα1 protein

Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes

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Cation−π Interaction: Its Role and Relevance in Chemistry, Biology, and Material Science

Cited by 967 publications

References 740 publications

Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms

Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms

Contribution of each Trp residue toward the intrinsic fluorescence of the Giα1 protein

Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes

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Contribution of each Trp residue toward the intrinsic fluorescence of the G_iα1 protein