title: DNA binding dynamics and energetics of cobalt, nickel, and copper metallopeptides.
abstract: We present molecular dynamics (MD) and Quantum Theory of Atoms in Molecules (QTAIM) analysis of the DNA binding properties of three metallopeptides to the Drew-Dickerson dodecamer DNA: Co(II) -Gly(1) -Gly(2) -His, Ni(II) -Gly(1) -Gly(2) -His and Cu(II) -Gly(1) -Gly(2) -His. Fairly extensive MD simulations were run on each system until a stable binding mode for each ligand was sampled. Clustering analysis was used in an attempt to find representative structures for the most populated clusters sampled during the MD, and a QTAIM analysis was performed. Additionally, MM-PBSA analysis was performed to obtain approximate binding energies for each complex. The results suggest that stable DNA-metallopeptide complexes are formed with each of the three ligands, and that the most stable interaction is with Co(GGH), then Ni(GGH), and finally Cu(GGH). Bond Critical Points (BCP) information between the minor groove of the DNA and the metallopeptides shows an increase in electronic density between Gly(1) , the His residues, and the oxygen atoms of the thymine nucleotide. Overall, we present a detailed theoretical study of the specific interactions involved and the binding properties of each complex formed.
authors.affiliation: Department of Medicinal Chemistry, L. S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112 (USA).
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Galindo-Murillo
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Cheatham
mesh_terms: D000595:Amino Acid Sequence; D016000:Cluster Analysis; D003035:Cobalt / Q000737:chemistry* / Q000378:metabolism*; D003300:Copper / Q000737:chemistry*; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D045726:Metalloproteases / Q000737:chemistry / Q000378:metabolism*; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009532:Nickel / Q000737:chemistry*; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry
chemical_list: D003035:Cobalt; D003300:Copper; D009532:Nickel; D004247:DNA; D045726:Metalloproteases; D013941:Thymine
keywords: AMBER; DNA; DNA ligands; QTAIM; bioinorganic chemistry; transition metals