Benzene Forms Hydrogen Bonds with Water

HIGH RESOLUTION SPECTROSCOPY IN THE GAS PHASE: Even Large Molecules Have Well-Defined Shapes

▪ Abstract  A review of recent high-resolution microwave, infrared, and optical spectroscopy experiments demonstrates that remarkable progress has been made in the past 20 years in determining the equilibrium geometries of large polyatomic molecules and their clusters in the gas phase, and how these geometries change when the photon is absorbed. A special focus is on the dynamical information that can be obtained from such studies, particularly of electronically excited states.

Thermodynamics of aliphatic and aromatic hydrocarbons in water

Makhatadze and Privalov have analyzed the thermodynamics of transfer of aliphatic and aromatic hydrocarbons from the gas phase into water. Finding that the hydration free energy of aliphatic and aromatic hydrocarbons have different signs, they conclude that the mechanism causing hydrophobicity of these solutes is of a different nature. Here, we offer an alternative analysis of the dissolution of these non-polar compounds into water based on a recently published interpretation scheme for thermodynamic transfer functions. Our analysis shows that the hydrophobicity of aromatic and aliphatic hydrocarbons is qualitatively the same, i.e. its causes are the same namely the extremely high cohesive energy of water which overcomes the favorable solute-solute and solute-water interactions. However, both analyses conclude that the experimentally observed quantitative difference between the interactions of water with aliphatic and aromatic hydrocarbons, can be assigned to the formation of aromatic ring-water H-bonds.

A review of mutagenesis studies of angiotensin II type 1 receptor, the three-dimensional receptor model in search of the agonist and antagonist binding site and the hypothesis of a receptor activation mechanism

OBJECTIVE

To seek the mechanism whereby agonists, competitive antagonists and insurmountable antagonists affect the receptor function differently, by reviewing recent mutagenesis studies of angiotensin II type 1 receptor (AT1) in which the binding of the agonist and antagonists and receptor signaling were affected.

AT1 RECEPTOR STRUCTURE AND LIGAND BINDING SITES

We built a model of seven transmembrane spanning domains of the AT1 receptors using bacteriorhodopsin as a template. The carboxy terminal of angiotensin II binds to Lys199 in transmembrane domain 5, whereas the guanidinium group of Arg2 binds to Asp281 in transmembrane domain 7. Results of studies using mutagenesis supporting proposed ligand-docking models are discussed. HYPOTHESIS FOR THE LIGAND-INDUCED RECEPTOR SIGNALING MECHANISM: We submit a set of hypotheses for a mechanism whereby the ligand binding induces changes in the receptor conformation by the rotation of transmembrane helices as the initial event for the subsequent activation of a G protein. In this mechanism antagonists are not capable of rotating the helices but agonists are able to do so, which results in the formation of a hydrogen bond between Asp74 in transmembrane domain 2 and Tyr292 in transmembrane domain 7. This mechanism also provides plausible explanation for the activation of monoamine receptors.

COMPETITIVE AND INSURMOUNTABLE ANTAGONISTS

Competitive antagonists share the same binding sites with agonists, but insurmountable antagonists do not, and binding of the latter does not preclude agonist binding, for example, to Asp281.

CONCLUSION

This hypothesis of the intrareceptor signaling mechanism and the receptor model indicate that some amino acid residues essential for the signaling play their roles in the intrareceptor activation mechanism, whereas others participate directly in ligand binding.

Computational investigations of protein denaturation: apomyoglobin and chaotrope-arene interactions

Molecular dynamics (MD) and Monte Carlo (MC) simulations are being used to investigate protein denaturation. The calculations use the AMBER/OPLS force field with explicit representation of the solvent via the TIP3P and TIP4P models of water. The thermal denaturation of apomyoglobin has been followed in two 500 ps MD simulations at 85 °C. The resultant structures provide a detailed model of a molten globule, and close agreement is obtained with experimental data on the helical content of both native apomyoglobin and the low pH folding intermediate. The mechanism of protein denaturation by chaotropic agents is also being pursued. The possibility of direct contact between the chaotropes and aromatic sidechains is supported by MC computations of free energy profiles for the approach of urea and guanidinium ion to aromatic hydrocarbons in water.

Solvent Effects on a Diels-Alder Reaction Involving a Cationic Diene: Consequences of the Absence of Hydrogen-Bond Interactions for Accelerations in Aqueous Media

In order to study the influence of hydrogen-bond interactions on the accelerations of Diels-Alder reactions in water and highly aqueous mixed solvent systems, second-order rate constants for the Diels-Alder reaction of acridizinium bromide (1a) with cyclopentadiene (CP) have been measured in aqueous media and organic solvents. Only modest rate accelerations were found in water-rich media. This is attributed to the absence of hydrogen-bonding groups in the reactants. Comparison with cycloadditions of CP with 9-carbomethoxyacridizinium bromide (1b), acrylonitrile (3), and methyl vinyl ketone (4), which do contain hydrogen-bond acceptors, reveals substantially larger aqueous accelerations. These results demonstrate that hydrogen bonding is a major factor in aqueous accelerations. Also rate constants for the cycloaddition of CP to 1a in surfactant solutions were determined. Micellar catalysis is observed in SDS solutions, due to binding of both the diene and the dienophile to the anionic micellar surface.

Structure-based design of achiral, nonpeptidic hydroxybenzamide as a novel P2/P2' replacement for the symmetry-based HIV protease inhibitors

A combination of structure-activity studies, kinetic analysis, X-ray crystallographic analysis, and modeling were employed in the design of a novel series of HIV-1 protease (HIV PR) inhibitors. The crystal structure of a complex of HIV PR with SRSS-2,5-bis[N-(tert-butyloxycarbonyl)amino]-3,4-dihydroxy-1, 6-diphenylhexane (1) delineated a crucial water-mediated hydrogen bond between the tert-butyloxy group of the inhibitor and the amide hydrogen of Asp29 of the enzyme. Achiral, nonpeptidic 2-hydroxyphenylacetamide and 3-hydroxybenzamide groups were modeled as novel P2/P2' ligands to replace the crystallographic water molecules and to provide direct interactions with the NH groups of the Asp29/129 residues. Indeed, the symmetry-based inhibitors 7 and 19, possessing 3-hydroxy and 3-aminobenzamide, respectively, as a P2/P2' ligand, were potent inhibitors of HIV PR. The benzamides were superior in potency to the phenylacetamides and have four fewer rotatable bonds. An X-ray crystal structure of the HIV PR/7 complex at 2.1 A resolution revealed an asymmetric mode of binding, in which the 3-hydroxy group of the benzamide ring makes the predicted interaction with the backbone NH of Asp29 on one side of the active site only. An unexpected hydrogen bond with the Gly148 carbonyl group, resulting from rotation of the aromatic ring out of the amide plane, was observed on the other side. The inhibitory potencies of the benzamide compounds were found to be sensitive to the nature and position of substituents on the benzamide ring, and can be rationalized on the basis of the structure of the HIV PR/7 complex. These results partly confirm our initial hypothesis and suggest that optimal inhibitor designs should satisfy a requirement for providing polar interactions with Asp29 NH, and should minimize the conformational entropy loss on binding by reducing the number of freely rotatable bonds in inhibitors.

Secondary structure and NMR assignments of Bacillus circulans xylanase

Bacillus circulans xylanase (BCX) is a member of the family of low molecular weight endo-beta-(1,4)-xylanases. The main-chain 1H, 13C, and 15N resonances of this 20.4-kDa enzyme were assigned using heteronuclear NMR experiments recorded on a combination of selectively and uniformly labeled protein samples. Using chemical shift, NOE, J coupling, and amide hydrogen exchange information, 14 beta-strands, arranged in a network of three beta-sheets, and a single alpha-helix were identified in BCX. The NMR-derived secondary structure and beta-sheet topology agree closely with that observed in the crystal structure of this protein. The HN of Ile 118 has a strongly upfield-shifted resonance at 4.03 ppm, indicative of a potential amide-aromatic hydrogen bond to the indole ring of Trp 71. This interaction, which is conserved in all low molecular weight xylanases of known structure, may play an important role in establishing the active site conformation of these enzymes. Following hen egg white and bacteriophage T4 lysozymes, B. circulans xylanase represents the third family of beta-glycanases for which extensive NMR assignments have been reported. These assignments provide the background for detailed studies of the mechanism of carbohydrate recognition and hydrolysis by this bacterial xylanase.

Distribution of solvent and ligand molecules around aromatic side chains in proteins and its implication on carbonic anhydrase catalytic mechanism

Interactions between aromatic phenylalanine, tyrosine and tryptophan residues and water as well as ligand molecules were analyzed by a computer search of a large number of high resolution structures in the protein data bank. Water molecules and oxygen ligands have a preference for the edges of the aromatic residues, but the distribution of carbon ligands around the aromatic rings is different. The more hydrophilic tyrosine, followed by tryptophan, has the highest frequency of water contacts. However the situation is reversed for ligand interactions where phenylalanine is the most active of the three aromatic residues. The results indicate that hydrogen bonding by water molecules to aromatic pi-electron does not occur in protein structures. The role of the conserved Trp 209 in the catalytic mechanism of carbonic anhydrase is discussed in consideration of the results from the data base search. Normally not considered as a catalytic residue, this tryptophan is proposed to participate in the physiologically important enzymatic interconversion of carbon dioxide and bicarbonate by stabilizing substrate coordination through van der Waals' interactions.

Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp

Cations bind to the pi face of an aromatic structure through a surprisingly strong, non-covalent force termed the cation-pi interaction. The magnitude and generality of the effect have been established by gas-phase measurements and by studies of model receptors in aqueous media. To first order, the interaction can be considered an electrostatic attraction between a positive charge and the quadrupole moment of the aromatic. A great deal of direct and circumstantial evidence indicates that cation-pi interactions are important in a variety of proteins that bind cationic ligands or substrates. In this context, the amino acids phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp) can be viewed as polar, yet hydrophobic, residues.