Narrow Results

The interactions of the four typical nucleotides with the metal ions Mg²⁺, Ca²⁺, Mn²⁺, Na⁺, and K⁺ were studied by using the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d,p) calculations in the PCM model. A lot of initial binding sites of the metal ions were designed and optimized to determine the most stable structures of the metal ion nucleotide compounds. It has been shown that the metal ions tend to attach at the center of the negatively charged atoms of the nucleotides. Furthermore, the vertical excitation energies of the metal ion nucleotide compounds were calculated at the same level with the TDDFT method, and also NBO charges were analyzed to understand the bonding characteristics between the metal ions and the nucleotides. That was also compared with the conclusion in the gas phase.

Photophysical properties of meso-tetrakis(4-N-methylpyridiniumyl)porphyrin (TMpyP4) and its metallocomplexes M(II)TMpyP4 (M = Zn, Cu, Ni, Co) bound to natural DNA and synthetic poly-, oligo- and mononucleotides are considered with a primary emphasis placed upon intermolecular interaction of the photoexcited porphyrins with the nearest environment. Quenching of the fluorescent S₁ (but not triplet T₁) state due to guanine to porphyrin electron transfer is observed for TMpyP4 intercalated between GC base pairs of the double-strand helixes, whereas in the case of TMpyP4 complexed with guanosine monophosphate (GMP) both S₁ and T₁ states of the porphyrin are quenched. Furthermore, a dependence of the efficiency of TMpyP4 triplet state quenching by the dissolved molecular oxygen from air on the porphyrin localization enables one to readily distinguish porphyrin groove binding mode from intercalation. Excited states of the TMpyP4 complexes with transition metals, in spite of their very short lifetimes, also interact with nucleic acid components by means of an axial ligand binding/release to/from the metal. A possible structure of the five-coordinate excited complex (“exciplex”) formed in case of CuTMpyP4 groove binding to some single- and double-strand polynucleotides is discussed.

Actin is a highly conserved cytoskeletal protein that is present in all eukaryotes. Polymerization of actin to filamentous actin is essential for numerous cellular processes. Abnormal actin dynamics are directly associated with a variety of diseases, including cancer, immunological and neurological disorders. However, the dynamics of actin are not fully understood. In this work, we study the effects of nucleotides and metal ions on conformation of F/G-actin using molecular dynamics (MD) simulations. Our results show that different nucleotides and metal ions change the conformation of actin. The state of Adenosine Triphosphate (ATP) binding on F-actin conformation is more stable than G-actin. The D-loop has a large fluctuation when ${\text{Ca}}^{2+}$ binds to G-ATP-actin than ${\text{Mg}}^{2+}$ binds. Adenosine Diphosphate (ADP) binding leads to a stronger residual correlation on F-actin conformation, while it is opposite on G-actin. In addition, the detailed interactions between nucleotides and adjacent residues are discussed on different states of actin. This work provides a structural basis for understanding how the different nucleotides/metal ions binding influences the conformation of actin.