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Recognition of the methylated regions of the DNA plays an important role in the epigenetic processes. We analyze the interactions between the methylated DNA and the methyl-CpG-binding proteins using two models. The first model was built from a methylated or non-methylated cytosine, a guanine and an arginine residue in the experimental arrangement. We applied the M06L density functional method with a small, polarized double-ζ basis set for the geometry optimizations, and the MP2 method with polarized triple-ζ basis set for the energy calculations. The second model was built from two methylcytosines, guanines, guanidinium groups plus an additional carboxyl group in the experimental arrangement. We applied the B3LYP method with a small, polarized double-ζ basis set for the geometry optimizations and thermal corrections. The single-point energies were obtained from dual-hybrid dRPA75 and dRPA@PBE0 calculations supplemented by a moderately large polarized triple-ζ basis set. The hydration effects were modeled by adding explicit water molecules. These calculations revealed that the hydrophobic interaction has the largest contribution to the Gibbs interaction energy and turns the arginine side chains into hydrogen bonding position. Our results show that the translation of the protein along the DNA double helix is sterically hindered by the contact of its arginine side chains with the methyl groups of the methyl cytosines. This supports a hopping mechanism for the searching movement of the protein along the DNA. [ABSTRACT FROM AUTHOR]

Glycoproteins play a central role in the immune response. In this study, we focus on the core of the common O-linked mucin-type glycopeptides. It has been observed that glycosylation stabilizes the protein in a stiffened, extended structure. We provide a unified picture for the conformation and stabilization of the O-glycosidic linkage using O-(2-acetylamino-2-deoxy-α- or -β- d-galacto- or -mannopyranosyl)- N-acetyl- l-serinamide model structures. We have calculated equilibrium geometries of the model structures with the B3LYP/6-31G(2 df, p) method suggested in the Gaussian-4 theory. According to the relative energies, we confirm that the GalNAc-Ser linkage is more stable than its mannose analogues. The natural preference for the α-GalNAc-Ser over the β-GalNAc-Ser anomers can be explained by entropic effects. We explored the hydrogen bonding patterns on the carbohydrate unit calculating highly accurate dRPA@PBE0.25 and dRPA75 energies and found that in some cases, the acetamido group can be fixed by hydrogen bonding from the (O3)H atom, but in most of the cases, it can rotate more freely. The torsion angles in the glycosidic linkage show that the linkage is stiffened more in the α-anomers and the most in the α-GalNAc-Ser structure because of the steric strains in the axial position and by two or three intramolecular hydrogen bonds. We also found that although, in our gas-phase model geometries, the peptide backbone prefers to be in a γ-turn, a structural water molecule can stabilize a polyproline II helix of a proline-rich sequence, a β-sheet, or more likely random coils. [ABSTRACT FROM AUTHOR]

Theoretical and experimental gas-phase studies of carbohydrates show that their hydroxyl groups are located in homodromic partial rings that resemble cooperative hydrogen bonds, albeit with long H...O distances and small O-H...O angles. On the other hand, anecdotal experience with disaccharide crystal structures suggested that these clockwise 'c' or counter-clockwise (reverse 'r') sequences are not prevalent in the crystalline state. The situation was clarified with quantum mechanics calculations in vacuum and in continuum solvation, as well as Atoms-In-Molecules analyses. From the experimental side, the Cambridge Structural Database was searched. Geometric criteria for these sequences were developed. A criterion based on 120° ranges of hydroxyl orientations accepted 4% of sequences as having 'c,c' or 'r,r' orientations instead of the 7% expected based on chance. Criteria based on an O-H...O angle > 90° and a 90° lower limit of the absolute value of the H-O-C...H improper torsion accepted 7.0% of the 358 sequences as 'c,c' or 'r,r'. Highly variable orientation of the hydroxyl groups in crystals was seen to depend mostly on strong inter-residue or intermolecular hydrogen bonds. That lack of specific orientation in general for the crystal structures was supported by the solvated calculations that showed very little variation in the energy when one of the hydroxyl groups in 1,2-dihydroxycyclohexane was rotated. The vacuum calculations found the energy to vary with rotation by more than 4 kcal/mol, confirming the gas-phase experiments and calculations on more complicated molecules. Molecules examined in some detail include scyllo inositol and native and methylated cellobiose. [ABSTRACT FROM AUTHOR]

He(I) and He(II) photoelectron spectra of phenylphosphine and phenylarsine have been investigated and assigned. The rotational barrier of the phosphino group has been investigated at the MP2/6-31G(d,p)//MP2/6-31G(d,p) and HF/6-31G(d,p)//HF/6-31G(d,p) levels of theory, and that of the arsino group at the HF/6-31G(d,p)//6-31G(d,p) levels of theory. The rotational barrier of the two molecules is nearly the same. The energy difference between the two possible conformers of the molecules is low (1.5 kJ/mol at the MP2/6-31G(d,p) level of theory), allowing nearly free rotation about the P-C bond. The photoelectron spectrum cannot be interpreted by considering the most stable rotamer, but all possible conformers should be taken into account. The present interpretation is consistent with the small n- π interaction concluded from other investigations. The rotational barrier of o-phosphinophenol is significantly larger than for phenylphosphine, and the photoelectron spectrum of this compound can be interpreted by considering a single conformer, and no appreciable interaction between the π-system of the ring and the phosphorus lone pair. [ABSTRACT FROM AUTHOR]