Penta-coordinate phosphorous compounds and biochemistry

A COMPARISON OF THE STEREOISOMERIC PENTA-COORDINATED PHOSPHORUS INTERMEDIATES FORMED FROM 19 DIMETHOXYL N-PHOSPHORYL AMINO ACIDS BY DFT CALCULATIONS

N-phosphoryl amino acids (PAAs) are important species in the origin of life that self-catalyze and self-assemble into polypeptides and polynucleotides under mild conditions. Both experimental and theoretical studies have shown that a penta-coordinated phosphorus intermolecular mixed carboxylic-phosphoric anhydride (IMCPA) is formed as the common intermediate in these reactions. In this work, the mechanism for the formation of stereoisomeric IMCPAs from PAAs is investigated using density functional theory (DFT) calculations at the B3LYP/6-311+G(d,p) theoretical level. The molecular structures of the cis- and the trans-IMCPAs, as well as the transition states of the two stereochemical reaction pathways, were characterized in detail. The results showed that the hydroxyl groups of PAAs were situated in favorable positions for attacking the phosphorus atom from two sides of the phosphoryl group, resulting in the formation of the cis-IMCPA and the trans-IMCPA, respectively. The trans-isomers were predicted to be more likely to undergo a further reaction involving an ester exchange on the phosphorus than the cis-isomers. By comparing the relative energies of the IMCPAs and the activation energies, the trans-IMCPAs were computed to be more stable than the cis-IMCPAs, but the energy barriers for the formation of the trans- and the cis-isomers were similar. This work is expected to shed light on the stereochemical effect involved in the chemical evolution of biomolecules.

Modeling kinase-substrate specificity: implication of the distance between substrate nucleophilic oxygen and attacked phosphorus of ATP analog on binding affinity

Molecular dynamics simulations were performed on modeled kinase-substrate complexes in an attempt to establish a relationship between structural features and binding ability of the complexes. We found that the monitored distance between substrate nucleophilic oxygen (OG) and attacked phosphorus (PG) of ATP analog correlated closely with the binding affinity. With reference to 3.3 A, the van der Waals sum of oxygen and phosphorus, the calculated distances of good substrates were close to it whereas those of poor substrates were far apart from it. Therefore, it is reasonable to consider the OG-PG distance as a potential criterion to prefigure the kinase-substrate binding specificity and the simple computational techniques may work as an easy approach to distinguish good substrates from weak or poor substrates.

Molecular modeling on DNA cleavage activity of seryl-histidine and related dipeptide

Molecular interaction between seryl-histidine (or seryl-histidine related dipeptides) and DNA model molecule 5'-TpTpdC-3' was studied by a molecular docking procedure. The key structural features of DNA cleaving activity were investigated.