Search

Post-translational modification of proteins by N-phosphorylation of the basic amino acid residues plays important roles in biological processes. The high-energy P-N bond might have contributed to the evolution of prebiotic chemistry. N-phosphoryl amino acids (PAAs) can serve as interesting small molecular models for the study of P-N bonds in prebiotic chemical evolution. PAAs are capable of simultaneously producing several important biomolecules such as polypeptides and oligonucleotides under mild reaction conditions. In this review, we describe the chemistry of PAAs, discusse their likely prebiotic origins and their reactivity and how they relate to biological P-N bond species. We also depict a possible prebiotic scenario mediated by PAAs in which PAAs may have acted as one of the essential forces driving prebiotic biomolecules to the first protocell.

In this work, n-alkylamines (number of carbon atoms ranging from 3 to 10) were investigated in detail by molecular modeling as spacers for intercalating porphyrins into α-zirconium phosphate (α-ZrP). Pre-intercalated n-alkylamines can form either a flat monolayer or a canted bilayer in the gallery of α-ZrP. Based on the interlayer state and intercalative potential of the two modes in α-ZrP, it is suggested that the flat monolayer is a better spacer than the bilayer and that n-propylamine (PA) and n-butylamine (BA) in mobile monolayers are the best spacers among the n-alkylamines studied, as is also found experimentally. The intercalation behavior of TMPyP [5,10,15,20-tetrakis (1-methylpyridinium-4-yl) porphyrin] and several other porphyrins was investigated by calculating the intercalative potential. The calculated results showed that the porphyrins were densely packed in a canted monolayer model, and an increase of polarity of the substituent would facilitate the intercalation of the porphyrins.

In this work, molecular modeling methods have been applied to the interaction characterization of polypyridyl transitional-metal complexes with the oligonucleotide (B-DNA fragment). In order to explore the factors governing the groove recognition and intercalative depth, we establish a simple and practical docking method (step-by-step docking operation) to obtain potential curves while making complexes inset into B-DNA along an assigned path. Energy values in the potential curve are obtained from energy minimization of binding geometries. Modeling results clearly show that the optimum binding conformation corresponding to the global minimum in the potential curve for each complex is found to correlate well with the experimental results. Our results also confirm that minor changes of the ligand structure can lead to profound influences on binding geometries, so the molecular shape of the complexes is a predominant factor in governing the binding mode. Moreover, we find that the vdW force and “water molecular effect” are strongly associated with molecular-shape selection in our model. These results complement and extend the knowledge of the nature of these complexes binding to B-DNA. Figure Schematic illustration of metal complexes bound to B-DNA. The complexes are intercalated into the A 5T 6/T 6A 5 base step via a “head-on” fashion

In this paper, molecular modeling methods have been applied to the structural characterization of the interaction of chiral metal complexes [Co(phen)2dppz]3+{where phen=1,10-phenanthroline, dppz=dipyrido[3,2-a:2′,3′-c]phenazine} and [Co(phen)2tpphz]3+{where phen=1,10-phenanthroline, tpphz=tetrapyrido[3,2-a:2′,3′-c:3″,2″-h:2‴,3‴-j] phenazine} with the oligonucleotide (B-DNA fragment). The nature of two kinds of binding, a subject of currently controversy, has been explored. Barton et al. have proposed that there is an enantioselective DNA binding by the octahedral complexes and intercalative access by these complexes from the major groove. Norden et al. have suggested that both enantiomers bind extremely strongly to DNA from the minor groove without any noticeable enantioselectivity. Our results support and extend structural models of the minor groove based upon Norden's studies and Barton's enantioselectivity model.