Amino Acid Structural Features Research Articles

Quantum chemical study of the molecular structure of the sodium dodecylsulfate complexes with glycine and cysteine

The quantum chemical modeling of sodium dodecylsulfate (DDSNa) complexes with glycine (Gly) and cysteine (Cys) is carried out at the DFT/B97D level using the Grimme hybrid exchange-correlation functional with a dispersion correction and the 6-311++G(2d,2p) basis set. The structure of the Gly and Cys molecular and zwitterionic forms is examined. The structures and the formation energies of DDSNa…Gly and DDSNa…Cys complexes are determined. The effect of the amino acid structural features on the stability of the complexes they form with DDSNa is analyzed. The NBO analysis of the electron density distribution in the DDSNa molecule is performed.

Quantification of the influence of single-point mutations on haloalkane dehalogenase activity: a molecular quantum similarity study.

Controlled modifications in certain protein amino acid residues can lead to changes in their function and stability. Amino acid structural features and their relation to these changes were examined by using quantum molecular similarity techniques. The effect of deliberate mutations in position 172 of the haloalkane dehalogenase enzyme, yielding to variations on the dehalogenation of 1,2-dibromoethane, was studied qualitatively and quantitatively using molecular quantum similarity techniques. A valuable classification of the residues according to their effect on activity was obtained by representing the optimal two-dimensional classical scaling solution. In addition, satisfactory quantitative relationships were found, comparable to those attained by previous studies on this same data set using other techniques. Molecular quantum similarity analysis provides a consistent, unbiased, and homogeneous set of molecular descriptors and is a feasible alternative to the use of physicochemical properties.

Resin probe analysis: II. Amino acid coupling reactions

Resin probe analysis has been employed to evaluate the availability of dicyclohexylcarbodiimide (DCC)-activated amino acids, the relationship between coupling time and reaction yield, and the influence of triethylamine (TEA) concentration on peptide bond formation. Results are presented for five amino acids which indicate that the coupling reactions plateau within 5 min, and no significant increase in yield is observed for longer incubation times. Large decreases in coupling yield (70–90%) were observed at concentrations of TEA above 0.01 m. Inactivation appears to be dependent in part upon amino acid structural features. In the absence of TEA, DCC-activated t-butyloxycarbonyl (Boc)-glycine was stable in the activated state for hours. peptide bond formation showed little or no amino acid concentration-dependence in the range of 0.01–0.04 m. Resin probe experiments provide quantitative data on reaction progress and factors that influence the availability and reactivity of activated amino acids.