Benzene Forms Hydrogen Bonds with Water

Theoretical study of inhibition of adenosine deaminase by (8R)-coformycin and (8R)-deoxycoformycin

Molecular dynamics and free energy simulations were performed to examine the binding of (8R)-deoxycoformycin and (8R)-coformycin to adenosine deaminase. The two inhibitors differ only at the 2' position of the sugar ring; the sugar moiety of conformycin is ribose, while it is deoxyribose for deoxycoformycin. The 100 ps molecular dynamics trajectories reveal that Asp 19 and His 17 interact strongly with the 5' hydroxyl group of the sugar moiety of both inhibitors and appear to play an important role in binding the sugar. The 2' and 3' groups of the sugars are near the protein-water interface and can be stabilized by either protein residues or water. The flexibility of the residues at the opening of the active site helps to explain the modest difference in binding of the two inhibitors and how substrates/inhibitors can enter an otherwise inaccessible binding site.

How are close residues of protein structures distributed in primary sequence?

Structurally neighboring residues are categorized according to their separation in the primary sequence as proximal (1-4 positions apart) and otherwise distal, which in turn is divided into near (5-20 positions), far (21-50 positions), very far ( > 50 positions), and interchain (from different chains of the same structure). These categories describe the linear distance histogram (LDH) for three-dimensional neighboring residue types. Among the main results are the following: (i) nearest-neighbor hydrophobic residues tend to be increasingly distally separated in the linear sequence, thus most often connecting distinct secondary structure units. (ii) The LDHs of oppositely charged nearest-neighbors emphasize proximal positions with a subsidiary maximum for very far positions. (iii) Cysteine-cysteine structural interactions rarely involve proximal positions. (iv) The greatest numbers of interchain specific nearest-neighbors in protein structures are composed of oppositely charged residues. (v) The largest fraction of side-chain neighboring residues from beta-strands involves near positions, emphasizing associations between consecutive strands. (vi) Exposed residue pairs are predominantly located in proximal linear positions, while buried residue pairs principally correspond to far or very far distal positions. The results are principally invariant to protein sizes, amino acid usages, linear distance normalizations, and over- and underrepresentations among nearest-neighbor types. Interpretations and hypotheses concerning the LDHs, particularly those of hydrophobic and charged pairings, are discussed with respect to protein stability and functionality. The pronounced occurrence of oppositely charged interchain contacts is consistent with many observations on protein complexes where multichain stabilization is facilitated by electrostatic interactions.

Atomic and residue hydrophilicity in the context of folded protein structures

Water-protein interactions drive protein folding, stabilize the folded structure, and influence molecular recognition and catalysis. We analyzed the closest protein contacts of 10,837 water molecules in crystallographic structures to define a specific hydrophilicity scale reflecting specific rather than bulk solvent interactions. The tendencies of different atom and residue types to be the nearest protein neighbors of bound water molecules correlated with other hydrophobicity scales, verified the relevance of crystallographically determined water positions, and provided a direct experimental measure of water affinity in the context of the folded protein. This specific hydrophilicity was highly correlated with hydrogen-bonding capacity, and correlated better with experimental than computationally derived measures of partitioning between aqueous and organic phases. Atoms with related chemistry clustered with respect to the number of bound water molecules. Neutral and negatively charged oxygen atoms were the most hydrophilic, followed by positively-charged then neutral nitrogen atoms, followed by carbon and sulfur atoms. Agreement between observed side-chain specific hydrophilicity values and values derived from the atomic hydrophilicity scale showed that hydrophilicity values can be synthesized for different functional groups, such as unusual side or main chains, discontinuous epitopes, and drug molecules. Two methods of atomic hydrophilicity analysis provided a measure of complementarity in the interfaces of trypsin:pancreatic trypsin inhibitor and HIV protease:U-75875 inhibitor complexes.

Influences of peptide side chains on the metal ion binding site in metal ion-cationized peptides: Participation of aromatic rings in metal chelation

Aromatic side chains on amino acids influence the fragmentations of cationic complexes of doubly charged metal ions and singly deprotonated peptides. The metal ion interacts with an aromatic side chain and binds to adjacent amide nitrogens. When fragmentation occurs, this bonding leads to the formation of abundant metal-containing a-type ions by reactions that occur at the sites of amino acids that contain the aromatic side chain. Furthermore, formation of metal-containing immonium ions of the amino acids that contain the aromatic side chain also are formed. The abundant a-type ions may be useful in interpretation strategies in which it is necessary to locate in a peptide the position of an amino acid that bears an aromatic side chain.

Test of the contribution of an amino-aromatic hydrogen bond to protein function

Hydrogen bonds which form between a hydrogen bond donor and an aromatic ring as acceptor are thought to contribute to the stability and function of proteins. We have tested the function of such an interaction in a highly homologous pair of proteins, cellular retinol-binding protein (CRBP) and cellular retinol-binding protein, type II [CRBP(II)]. Both proteins bind the ligand all-trans-retinal with comparable affinities, but CRBP has an approximately 100-fold higher affinity for all-trans retinal. The greater affinity of CRBP for all-trans-retinol has been attributed to the presence of an amino-aromatic hydrogen bond, which is absent in CRBP(II). We have generated a pair of mutant proteins, in which the amino-aromatic interaction was removed from CRBP and introduced into CRBP(II). Spectral analyses of retinol when bound to the wild-type and mutant CRBP suggested that it adopted an identical conformation within both proteins, a conformation that was distinct from that of retinol bound to CRBP(II), both wild-type and mutant. Unexpectedly, the affinities of the mutant binding proteins for all-trans-retinol were indistinguishable from those of their corresponding wild-type proteins. Further, in ligand competition experiments, there were no observable differences between mutant and wild-type CRBP, or between mutant and wild-type CRBP(II), in their preferences for binding all-trans-retinol versus all-trans-retinal. The results of this direct test of the proposed function of an amino-aromatic hydrogen bond did not support a functional role for such bonds, at least in this system.

Extended electron distributions applied to the molecular mechanics of some intermolecular interactions

Extended electron distributions (XEDs) have been added to the molecular mechanics Coulombic term and applied to a selection of intermolecular interactions. The results from this approach have been compared with the commonly used atom-centred charges and more rigorous AM1-derived natural atom orbital point densities. The use of XEDs generally improves the simulation of experimental and ab initio results over the other two charge allocations and corrects geometries in those cases for which the others yield wrong results.

Energetics of interactions of aromatic hydrocarbons with water

The thermodynamics of transfer of aromatic (benzene, toluene) and aliphatic (ethane, propane, butane) hydrocarbons from the gas phase into water in the temperature range 5-125 degrees C have been analyzed in order to determine the net hydration effect of these compounds. In the case of the aromatic hydrocarbons the enthalpic contribution predominates over the entropic contribution to the Gibbs energy of hydration. This results in a negative value of the hydration Gibbs energy of aromatic hydrocarbons, in contrast to the positive Gibbs energy of hydration of aliphatic hydrocarbons. The different sign of the hydration Gibbs energies indicates that the mechanism causing hydrophobicity of aromatic hydrocarbons has different nature than that causing the hydrophobicity of aliphatic hydrocarbons. The comparison of hydration of aliphatic and aromatic hydrocarbons leads to the following thermodynamic parameters for these additional interactions between the benzene ring and water at 25 degrees C: enthalpy -5.4 kJ/mol, entropy 26.8 J/K mol and Gibbs energy -13.4 kJ/mol. The large enthalpic contribution to the Gibbs energy of hydration of aromatic hydrocarbons probably comes from the ability of the aromatic ring to accept hydrogens from water, forming hydrogen bonds.

High melatonin solubility in aqueous medium

The pineal hormone melatonin (5-methoxy-N-acetyl-tryptamine) has been reported to participate in important physiological processes. Although some of its biological actions seem to depend on a protein receptor at the membrane surface, melatonin is known to interact with a large variety of tissues and cells, suggesting that the molecule may not necessarily interact through a specific membrane receptor at a specific cell. Most discussions of melatonin activity have assumed that the molecule is highly hydrophobic. Contrary to belief, the present work shows that melatonin is soluble in a purely aqueous medium up to 5 x 10(-3) M and describes a new method of melatonin preparation which shows the high hydrophilicity of the molecule. The results presented will affect the current biological hypothesis on the need of a melatonin carrier in the blood stream or the mechanisms which allow the hormone to cross the cell membrane and interact at the level of the nucleus.

Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance

The most frequently occurring resistance of Gram-negative bacteria against tetracyclines is triggered by drug recognition of the Tet repressor. This causes dissociation of the repressor-operator DNA complex and enables expression of the resistance protein TetA, which is responsible for active efflux of tetracycline. The 2.5 angstrom resolution crystal structure of the homodimeric Tet repressor complexed with tetracycline-magnesium reveals detailed drug recognition. The orientation of the operator-binding helix-turn-helix motifs of the repressor is inverted in comparison with other DNA binding proteins. The repressor-drug complex is unable to interact with DNA because the separation of the DNA binding motifs is 5 angstroms wider than usually observed.

Molecular polarization maps as a tool for studies of intermolecular interactions and chemical reactivity

Maps for the interaction energy of acetone, pyrrole, furan, and pyridine with a positive unitary charge were computed using ab initio techniques, together with their molecular electrostatic potentials at the same points. The difference between the interaction and electrostatic potential maps yielded polarization maps for the molecules. Finally, maps for the interaction with a negative charge were obtained as the difference between the polarization and electrostatic potential maps. The calculations were carried out for three planes, 2 Bohr radii, 4 Bohr radii, and 8 Bohr radii from the plane containing the heavy atoms for all the molecules. At larger distances, the interaction and electrostatic maps resemble each other qualitatively; however, at shorter distances, where the polarization effects are more significant, the differences between the maps are notable. Interaction and polarization maps can be routinely evaluated for medium-sized molecules, and are likely to become an important tool in drug design and chemical reactivity.

Structures of base pairs with 5-(hydroxymethyl)-2'-deoxyuridine in DNA determined by NMR spectroscopy

Base pairs with 5-(hydroxymethyl)-2'-deoxyuridine (HMdU) opposite either adenine or guanine in a seven-base oligonucleotide duplex have been studied by NMR spectroscopy. When paired with A, the HMdU-A base pair is in Watson-Crick geometry. The hydroxymethyl group maintains a fixed orientation in which the oxygen is on the 5' side of the base. The energy-minimized structure indicates the presence of a hydrogen bond between the hydroxymethyl group and the N7 of the 5' guanine residue. When paired with guanine, HMdU-G is in a wobble configuration at low pH. The hydroxymethyl group is on the 3' side of the base, positioned to form an intramolecular hydrogen bond with its own O4 carbonyl. With increasing pH, HMdU-G is observed to ionize with an apparent pK value of 9.7. The high-pH structure is in a Watson-Crick configuration, with the HMdU residue in a position similar to that observed for HMdU-A. It is proposed that interresidue hydrogen bonding of the HMdU residue may stabilize aberrant base-pair configurations.

Conformational analysis of arachidonic and related fatty acids using molecular dynamics simulations

Arachidonic acid has recently gained attention as a result of current evidence indicating that it may play the role of a 'second messenger' in signal transduction processes. In order to gain insight into the mechanism behind its action, quenched molecular dynamics simulations were performed on arachidonic (20:4) and related fatty acids: linoleic (18:2), oleic (18:1), arachidic (20:0), and stearic (18:0). The angle-iron structure, representative of arachidonic acid in the crystal or very-low-temperature state, readily gave way at higher temperature to a dominant hairpin structure whereby the COOH end of arachidonic acid comes into close proximity with the C14-15 pi-bond resulting in a packed pi-bond-rich loop. The lowest energy conformer for arachidonic acid was found to be 10.65 kcal/mol below that of the energy-minimized crystal structure. In the case of saturated fatty acids, the crystal all-trans conformation remained the lowest energy form. Analysis of conformational energy contours for carbon-carbon torsion angles representative of fatty acids suggest that the flexibility of arachidonic acid is, in part, a result of the relative torsional freedom of C-C (single) bonds located between or adjacent to C = C (double) bonds. It is hypothesized that the ability of arachidonic acid to form packed structures with curved regions containing pi-bonds may allow for hydrophobic interactions with proteins, and/or hydrogen bonding between the pi-bonds of arachidonic acid and polar groups of the protein structures.

The nature of cation-pi binding: interactions between tetramethylammonium ion and benzene in aqueous solution

A combined quantum mechanical and molecular mechanical Monte Carlo simulation method was used to determine the free energy of binding between tetramethylammonium ion (TMA+) and benzene in water. The computed free energy as a function of distance (the potential of mean force) has two minima that represent contact and solvent-separated complexes. These species are separated by a broad barrier of about 3 kJ/mol. The results are in good accord with experimental data and suggest that TMA+ binds to benzene more favorably than to chloride ion, with an association constant of about 0.8 M-1.