Systematic elucidation of the second coordination sphere effect on the structure and properties of a blue copper protein, pseudoazurin

The rational structural and computational studies of a blue copper protein, pseudoazurin (PAz), and its Met16X (X = Phe, Leu, Val, Ile) variants gave clear functional meanings of the noncovalent interaction (NCI) through the second coordination sphere. The high-resolution X-ray crystal structures of Met16X PAz demonstrated that the active site geometry is significantly affected by the substitution of Met16, which is located within the NCI distance from the His81 imidazole ring at the copper active site. The computational chemistry calculations based on the crystal structure analyses confirmed that the NCI of S-π/CH-π (wild-type), π-π (Met16Phe), double CH-π (Met16Leu), and single CH-π (Met16Val and Met16Ile). The estimated interaction energies for the NCI demonstrated that the fine-tuning of the protein stability and Cu site properties form the second coordination sphere of PAz.

Hydrogen bonds of a water molecule in the second coordination sphere of amino acid metal complexes: Influence of amino acid coordination

The hydrogen bonds of free and coordinated amino acids with water molecule were studied by analyzing data in the crystal structures from the Cambridge Structural Database (CSD) and by quantum chemical calculations. The CSD data indicate bifurcated NH/O hydrogen bonds and O1/HO hydrogen bonds of coordinated oxygen. The O/HO hydrogen bonds of free zwitterions and non-coordinated carbonyl oxygen (O2/HO) in metal complexes form primarily linear, non-bifurcated hydrogen bonds. Calculated M06L-GD3/def2-TZVPP interaction energies for free zwitterions (glycine, cysteine, phenylalanine and, serine) and water molecule are in the range from -5.1 to -9.6 kcal/mol for NH/O and from -6.9 to -7.6 kcal/mol for O/HO interactions. Coordinated amino acids in neutral octahedral cobalt(III) complexes have NH/O interaction energies ca. -7.4 kcal/mol, independent of the amino acid. The singly and doubly charged complexes have stronger NH/O interactions; the strongest has energy of -16.9 kcal/mol. In the case of O1/HO hydrogen bond, the interaction energy decreases upon coordination; interactions are quite weak for neutral complexes (-2.2 to -2.6 kcal/mol). For O2/HO hydrogen bonds, all amino acids except serine show slightly stronger interaction in singly negative complexes (-6.3 to -8.0 kcal/mol), while interactions are weaker for neutral complexes (-2.8 to -4.4 kcal/mol), comparing to zwitterions.

Electrochemical Kinetics Support a Second Coordination Sphere Mechanism in Metal-Based Formate Dehydrogenase

Metal-based formate dehydrogenases are molybdenum or tungsten-dependent enzymes that catalyze the interconversion between formate and CO₂ . According to the current consensus, the metal ion of the catalytic center in its active form is coordinated by 6 S (or 5 S and 1 Se) atoms, leaving no free coordination sites to which formate could bind to the metal. Some authors have proposed that one of the active site ligands decoordinates during turnover to allow formate binding. Another proposal is that the oxidation of formate takes place in the second coordination sphere of the metal. Here, we have used electrochemical steady-state kinetics to elucidate the order of the steps in the catalytic cycle of two formate dehydrogenases. Our results strongly support the "second coordination sphere" hypothesis.

Dinuclear copper(II) complexes with derivative triazine ligands as biomimetic models for catechol oxidases and nucleases

The research reported herein focuses on the synthesis of two new Cu(II) complexes {[Cu₂(2-X-4,6-bis(di-2-picolylamino)-1,3,5-triazine], with X = butane-1,4-diamine (2) or N-methylpyrenylbutane-1,4-diamine (3)}, the latter with a pyrene group as a possible DNA intercalating agent. The structure of complex (3) was determined by X-ray crystallography and shows the dinuclear {Cu^II(μ-OCH₃)₂Cu^II} unit in which the Cu^II···Cu^II distance of 3.040 Å is similar to that of 2.97 Å previously found for 1, which contains a {Cu^II(μ-OH)₂Cu^II} structural unit. Complexes (2) and (3) were also characterized in spectroscopic and electrochemical studies, and catecholase-like activity were performed for both complexes. The kinetic parameters obtained for the oxidation of the model substrate 3,5-di-tert-butylcatechol revealed that the insertion of the spacer butane-1,4-diamine and the pyrene group strongly contributes to increasing the catalytic efficiency of these systems. In fact, K_ass becomes significantly higher, indicating that these groups influence the interaction between the complex and the substrate. These complexes also show DNA cleavage under mild conditions with moderate reaction times. The rate of cleavage (k_cat) indicated that the presence of butane-1,4-diamine and pyrene increased the activity of both complexes. The reaction mechanism seems to have oxidative and hydrolytic features and the effect of DNA groove binding compounds and circular dichroism indicate that all complexes interact with plasmid DNA through the minor groove. High-resolution DNA cleavage assays provide information on the interaction mechanism and for complex (2) a specificity for the unpaired hairpin region containing thymine bases was observed, in contrast to (3).