Electrostatic Regulation of Blue Copper Sites

<div> <p>In the last 50 years, the blue copper proteins became central targets of investigation. Extensive experiments focused on the first- and second-coordination spheres of Cu to probe the effect of local perturbations on its properties. We found that local electric fields, generated by charged residues evolutionarily placed throughout the protein edifice, constitute an additional significant factor regulating blue copper proteins. These fields are not random, but exhibit a highly specific directionality, negative with respect to Cu-S_Cys and Cu-S_Met in the Cu first shell. The field magnitude contributes to fine-tuning of the geometric and electronic properties of Cu sites in individual blue copper proteins. Specifically, the local electric fields evidently control the Cu-S_Met bond distance, Cu(II)-S_Cys bond covalency, and the energies of the frontier molecular orbitals, which, in turn, govern the Cu(II/I) reduction potential and the relative absorption intensities at 450 nm and 600 nm.</p> </div> <br>

Electrostatic Regulation of Blue Copper Sites

<div> <p>In the last 50 years, the blue copper proteins became central targets of investigation. Extensive experiments focused on the first- and second-coordination spheres of Cu to probe the effect of local perturbations on its properties. We found that local electric fields, generated by charged residues evolutionarily placed throughout the protein edifice, constitute an additional significant factor regulating blue copper proteins. These fields are not random, but exhibit a highly specific directionality, negative with respect to Cu-S_Cys and Cu-S_Met in the Cu first shell. The field magnitude contributes to fine-tuning of the geometric and electronic properties of Cu sites in individual blue copper proteins. Specifically, the local electric fields evidently control the Cu-S_Met bond distance, Cu(II)-S_Cys bond covalency, and the energies of the frontier molecular orbitals, which, in turn, govern the Cu(II/I) reduction potential and the relative absorption intensities at 450 nm and 600 nm.</p> </div> <br>

Alkali Uranyl Borates: Bond Length, Equatorial Coordination and 5f States

Three uranyl borates, UO2B2O4, LiUO2BO3 and NaUO2BO3, have been prepared by solid state syntheses. The influence of the crystallographic structure on the splitting of the empty 5f and 6d states have been probed using High Energy Resolved Fluorescence Detected X-ray Absorption Spectroscopy (HERFD-XAS) at the uranium M4-edge and L3-edge respectively. We demonstrate that the 5f splitting is increased by the decrease of the uranyl U-Oax distance, which in turn correlates with an increased bond covalency. This is correlated to the equatorial coordination change of the uranium. The role of the alkalis as charge compensating the axial oxygen of the uranyl is discussed.

Both Configuration and QM Region Size Matter: Zinc Stability in QM/MM Models of DNA Methyltransferase

Quantum-mechanical/molecular-mechanical (QM/MM) methods are essential to the study of metalloproteins, but the relative importance of sampling and degree of QM treatment in achieving quantitative predictions is poorly understood. We study the relative magnitude of configurational and QM-region sensitivity of energetic and electronic properties in a representative Zn²⁺metal binding site of a DNA methyltransferase. To quantify property variations, we analyze snapshots extracted from 250 ns of molecular dynamics simulation. To understand the degree of QM-region sensitivity, we perform analysis using QM regions ranging from a minimal 49-atom region consisting only of the Zn²⁺metal and its four coordinating Cys residues up to a 628-atom QM region that includes residues within 12 Å of the metal center. Over the configurations sampled, we observe that illustrative properties (e.g., rigid Zn²⁺removal energy) exhibit large fluctuations that are well captured with even minimal QM regions. Nevertheless, for both energetic and electronic properties, we observe a slow approach to asymptotic limits with similarly large changes in absolute values that converge only with larger (ca. 300-atom) QM region sizes. For the smaller QM regions, the electronic description of Zn²⁺binding is incomplete: the metal binds too tightly, is too stabilized by the strong electrostatic potential of MM point charges, and the Zn-S bond covalency is overestimated. Overall, this work suggests that efficient sampling with QM/MM in small QM regions is an effective method to explore the influence of enzyme structure on target properties. At the same time, accurate descriptions of electronic and energetic properties require a larger QM region than the minimal metal-coordinating residues in order to converge treatment of both metal-local bonding and the overall electrostatic environment.

Both Configuration and QM Region Size Matter: Zinc Stability in QM/MM Models of DNA Methyltransferase

Quantum-mechanical/molecular-mechanical (QM/MM) methods are essential to the study of metalloproteins, but the relative importance of sampling and degree of QM treatment in achieving quantitative predictions is poorly understood. We study the relative magnitude of configurational and QM-region sensitivity of energetic and electronic properties in a representative Zn²⁺metal binding site of a DNA methyltransferase. To quantify property variations, we analyze snapshots extracted from 250 ns of molecular dynamics simulation. To understand the degree of QM-region sensitivity, we perform analysis using QM regions ranging from a minimal 49-atom region consisting only of the Zn²⁺metal and its four coordinating Cys residues up to a 628-atom QM region that includes residues within 12 Å of the metal center. Over the configurations sampled, we observe that illustrative properties (e.g., rigid Zn²⁺removal energy) exhibit large fluctuations that are well captured with even minimal QM regions. Nevertheless, for both energetic and electronic properties, we observe a slow approach to asymptotic limits with similarly large changes in absolute values that converge only with larger (ca. 300-atom) QM region sizes. For the smaller QM regions, the electronic description of Zn²⁺binding is incomplete: the metal binds too tightly, is too stabilized by the strong electrostatic potential of MM point charges, and the Zn-S bond covalency is overestimated. Overall, this work suggests that efficient sampling with QM/MM in small QM regions is an effective method to explore the influence of enzyme structure on target properties. At the same time, accurate descriptions of electronic and energetic properties require a larger QM region than the minimal metal-coordinating residues in order to converge treatment of both metal-local bonding and the overall electrostatic environment.