OH Group Of Side Chain Research Articles

Structural effects on the OH-promoted fragmentation of methoxy-substituted 1-arylalkanol radical cations in aqueous solution: the role of oxygen acidity.

A kinetic and product study of the OH- -induced decay in H2O of the radical cations generated from some di-and tri-methoxy-substituted 1-arylalkanols (ArCH(OH)R*+) and 2- and 3-(3,4-dimethoxyphenyl)alkanols has been carried out by using pulse- and gamma-radiolysis techniques. In the 1-arylalkanol system, the radical cation 3,4-(MeO)2C6H3CH2-OH*+ decay at a rate more than two orders of magnitude higher than that of its methyl ether; this indicates the key role of the side-chain OH group in the decay process (oxygen acidity). However, quite a large deuterium kinetic isotope effect (3.7) is present for this radical cation compared with its a-dideuterated counterpart. A mechanism is suggested in which a fast OH deprotonation leads to a radical zwitterion which then undergoes a rate-determining 1,2-H shift, coupled to a side-chain-to-ring intramolecular electron transfer (ET) step. This concept also attributes an important role to the energy barrier for this ET, which should depend on the stability of the positive charge in the ring and, hence, on the number and position of methoxy groups. On a similar experimental basis, the same mechanism is suggested for 2,5-(MeO)2C6H3CH2OH*+ as for 3,4-(MeO)2C6H3CH2OH*+, in which some contribution from direct C-H deprotonation (carbon acidity) is possible. In fact, the latter process dominates the decay of the trimethoxylated system 2,4,5-(MeO)3C6H2CH2-OH*+, which, accordingly, reacts with OH- at the same rate as that of its methyl ether. Thus, a shift from oxygen to carbon acidity is observed as the positive charge is increasingly stabilized in the ring; this is attributed to a corresponding increase in the energy barrier for the intramolecular ET. When R=tBu, the OH- -promoted decay of the radical cation ArCH(OH)R*+ leads to products of C-C bond cleavage. With both Ar = 3,4- and 2,5-dimethoxyphenyl the reactivity is three orders of magnitude higher than that of the corresponding cumyl alcohol radical cations; this suggests a mechanism in which a key role is played by the oxygen acidity as well as by the strength of the scissile C-C bond: a radical zwitterion is formed which undergoes a rate-determining C-C bond cleavage, coupled with the intramolecular ET. Finally, oxygen acidity also determines the reactivity of the radical cations of 2-(3,4-dimethoxyphenyl)ethanol and 3-(3,4-dimethoxyphenyl)propanol. In the former the decay involves C-C bond cleavage, in the latter it leads to 3-(3,4-dimethoxyphenyl)propanal. In both cases no products of C-H deprotonation were observed. Possible mechanisms, again involving the initial formation of a radical zwitterion, are discussed.

Breaking and making of the S–S linkage via nucleophilic substitution.: An ab initio study

The energetics of nucleophilic opening and closing of protonated disulphide bridges has been studied for the case of two sulphur-containing (H 2S and CH 3SH) nucleophiles. The energetics of this reaction was compared to that of the nucleophilic opening and closing of disulphide bridges with thiolate ions: In the former case a not so good nucleophile is combined with an excellent leaving group, and in the latter case a superior nucleophile is combined with a relatively poor leaving group. The barrier heights for these S N2-type reactions were found to be comparable as calculated by ab initio MO methods. In addition, two oxygen-containing nucleophiles (H 2O, HCONH–CH[CH 2OH]–CONH 2) have also been studied in the following reaction: The water molecule is not nucleophilic enough to open the disulphide bridge. However, in a serine residue, in which the oxygen of the side-chain OH group is activated through backbone/side-chain hydrogen bonding, the hydroxy group is sufficiently nucleophilic to open the disulphide bridge, just like the sulphur-containing nucleophiles mentioned above.

The tyrosine corner: A feature of most greek key β‐barrel proteins

The Tyr corner is a conformation in which a tyrosine (residue "Y") near the beginning or end of an antiparallel beta-strand makes an H bond from its side-chain OH group to the backbone NH and/or CO of residue Y - 3, Y - 4, or Y - 5 in the nearby connection. The most common "classic" case is a delta 4 Tyr corner (more than 40 examples listed), in which the H bond is to residue Y - 4 and the Tyr chi 1 is near -60 degrees. Y - 2 is almost always a glycine, whose left-handed beta or very extended beta conformation helps the backbone curve around the Tyr ring. Residue Y - 3 is in polyproline II conformation (often Pro), and residue Y - 5 is usually a hydrophobic (often Leu) that packs next to the Tyr ring. The consensus sequence, then, is LxPGxY, where the first x (the H-bonding position) is hydrophilic. Residues Y and Y - 2 both form narrow pairs of beta-sheet H-bonds with the neighboring strand. delta 5 Tyr corners have a 1-residue insertion between the Gly and Tyr, forming a beta-bulge. One protein family has a delta 4 corner formed by a His rather than a Tyr, and several examples use Trp in place of Tyr. For almost all these cases, the protein or domain is a Greek key beta-barrel structure, the Tyr corner ends a Greek key connection, and it is well-conserved in related proteins. Most low-twist Greek key beta-barrels have 1 Tyr corner. "Reverse" delta 4 Tyr corners (H bonded to Y + 4) and other variants are described, all less common and less conserved. It seems likely that the more classic Tyr corners (delta 4, delta 5, and delta 3 Tyr, Trp, or His) contribute to the stability of a Greek key connection over a hairpin connection, and also that they may aid in the process of folding up Greek key structures.

Design of anticancer drugs using modeling techniques.

Flexibility of intercalation site geometries within a B-DNA helix was investigated in the twist-shift plane using energy minimization methods. The parameters optimized included sugar conformation, the glycosidic angles and phosphodiester torsion angles. Our calculations show several regions of energetically favorable intercalation geometries in the twist-shift plane. Modeling studies using interactive computer graphics and electrostatic potential surface compatibility provided initial hypotheses for the structures of the drug-DNA complexes. These hypotheses were supported and extended by energy minimizations of these complexes. Binding positions, conformational features and relative minimum binding energies of two anticancer drugs, mitoxantrone and bisantrene, were computed for intercalation complexes with DNA in the theoretically defined intercalation sites. Mitoxantrone intercalates DNA from the minor groove and the side chain OH or NH groups are involved in hydrogen bonds with the main chain phosphate groups of DNA, thereby cross-linking the complementary strands. The hydroxyl groups of mitoxantrone can also participate in hydrogen bonding with phosphate oxygens of another chain, thereby cross-linking DNA helices. Bisantrene intercalates DNA favorably from the major groove and the NH group of the dihydroimidazole ring can participate in hydrogen bonding with the phosphate oxygens of the backbone. These models are consistent with the physicochemical and electron microscopic studies of the interaction of mitoxantrone and bisantrene with DNA. Our results are now being used to guide the design of novel anticancer drugs that should interact with DNA in a manner similar to that proposed for our representative drugs.

The structure of bovine liver rhodanese: II. The active site in the sulfur-substituted and the sulfur-free enzyme

X-ray studies at 2.5 Å resolution show that the active site of bovine liver rhodanese is a depression between the two domains. In sulfur-substituted rhodanese the density of the essential Cys247 corresponds with that of a persulfide. Both sulfur atoms are interacting via hydrogen bonds with several peptide NH and side-chain OH groups. One side of the active site pocket contains mainly hydrophylic, the other side mainly hydrophobic residues. None of these hydrophylic or hydrophobic groups appears to interact strongly with the persulfide. Crystals of the sulfur-substituted enzyme were treated with cyanide, a sulfur acceptor. Subsequent difference Fourier studies show that the extra sulfur atom has been removed. Only minor conformational differences appear to exist between the two rhodanese species studied. These are a movement of the Sγ atom of Cys247 and some rearrangement of solvent molecules near the active site. The combination of these observations with the results of experiments performed by other investigators suggest a mechanism for sulfur transfer by rhodanese in which the thiol group of Cys247 is the essential nucleophile, whereas the positive charges on Arg186 and Lys249 act in various ways as “electrophilic assistants”. The transition state and the persulfide in the sulfur-substituted enzyme are stabilized by several hydrogen bonds.

Proton NMR, EPR and absorption spectra studies of palladium(II) and copper(II) complexes with L-alanyl-L-serine

The conformation of L-alanyl—L-serine has been established by proton NMR spectra for various pH ranges. A hydrogen bond between the hydroxyl and the carboxyl group was assumed in order to explain the particular stability of the serine residue rotamers, in which both groups are gauche to each other. A structure for the Pd(II) and Cu(II) complexes with Ala—Ser in various pH solutions has been proposed from the NMR, EPR and absorption spectra. The coordination ability of the hydroxyl group of the serine residue was found at higher pH region. The serine side-chain OH group interaction with the Pd(II) ion was suggested to be responsible for the unusual stability of the gauche rotamer of the serine residue, in the 1:1 complex at pH 3–10.

Enkephalin: conformational analysis by means of empirical energy calculations.

Low-energy conformations of methionine-enkephalin were generated by means of an empirical method of computation. Many compact conformations, including those containing various standard bends, were of comparable energy. However, one conformation was found to have a potential energy about 5 kcal/mol (21 X 10(3) J/mol) below that of the large group of compact conformations. In this conformation, the 3-glycyl and 4-phenylalanyl residues form a bend of type II'. The conformation is stabilized by a hydrogen bond between the OH group of the 1-tyrosine side chain and the C==O group of 3-glycine or 4-phenylalanine. The phenylalanine and methionine side chains are relatively unrestricted. The conformation is consistent with published nuclear magnetic resonance parameters--coupling constants, temperature dependence of the chemical shift, and spin-lattice relaxation times. It is likely that the molecule undergoes a conformational change when it is bound to the receptor. Leucine-enkephalin appears to have the same conformation as its methionine homolog.