More Like this

1. Efficient localization of a native metal ion within a protein by Cu ²⁺ -based EPR distance measurements

   https://doi.org/10.1039/c8cp07143h  

   Gamble Jarvi, Austin; Cunningham, Timothy F.; Saxena, Sunil (May 2019, Physical Chemistry Chemical Physics)

   Electron paramagnetic resonance (EPR) based distance measurements have been exploited to measure protein–protein docking, protein–DNA interactions, substrate binding and metal coordination sites. Here, we use EPR to locate a native paramagnetic metal binding site in a protein with less than 2 Å resolution. We employ a rigid Cu 2+ binding motif, the double histidine (dHis) motif, in conjunction with double electron electron resonance (DEER) spectroscopy. Specifically, we utilize a multilateration approach to elucidate the native Cu 2+ binding site in the immunoglobulin binding domain of protein G. Notably, multilateration performed with the dHis motif required only the minimum number of four distance constraints, whereas comparable studies using flexible nitroxide-based spin labels require many more for similar precision. This methodology demonstrates a significant increase in the efficiency of structural determinations via EPR distance measurements using the dHis motif. 

   more » « less
2. Design of a light and Ca ²⁺ switchable organic–peptide hybrid

   https://doi.org/10.1073/pnas.2411316122  

   Khaleel, Zinah_Hilal; No, Young_Hyun; Kim, Nam_Hyeong; Bae, Do_Hyun; Wu, Yibing; Kim, Suhyeon; Choi, Hojae; Lee, Da_Eun; Jeong, Se_Yun; Ko, Yoon-Joo; et al (January 2025, Proceedings of the National Academy of Sciences)

   The design of organic–peptide hybrids has the potential to combine our vast knowledge of protein design with small molecule engineering to create hybrid structures with complex functions. Here, we describe the computational design of a photoswitchable Ca²⁺-binding organic–peptide hybrid. The designed molecule, designated Ca²⁺-binding switch (CaBS), combines an EF-hand motif from classical Ca²⁺-binding proteins such as calmodulin with a photoswitchable group that can be reversibly isomerized between a spiropyran (SP) and merocyanine (MC) state in response to different wavelengths of light. The MC/SP group acts both as a photoswitch as well as an optical sensor of Ca²⁺binding. Photoconversion of the SP to the corresponding MC unmasks an acidic phenol, which CaBS uses as an integral part of both its Ca²⁺-binding site as well as its tertiary and quaternary structure. By design, the SP state of CaBS is monomeric, while the Ca²⁺-bound form of the MC state is an obligate dimer, with two Ca²⁺-binding sites formed at the interface of a domain-swapped dimer. Thus, light and Ca²⁺were expected to serve as an “AND gate” that powers a change in backbone structure/dynamics, oligomerization state, and fluorescence properties of the designed molecule. CaBS was designed using Rosetta and molecular dynamics simulations, and experimentally characterized by nuclear magnetic resonance, isothermal titration calorimetry, and optical titrations. These data illustrate the potential of combining small molecule engineering with de novo protein design to develop sensors whose conformation, association state, and optical properties respond to multiple environmental cues. 

   more » « less
3. Magnetic transitions in exotic perovskites stabilized by chemical and physical pressure

   https://doi.org/10.1039/C9TC06976C  

   Ma, Yalin; Molokeev, Maxim S.; Zhu, Chuanhui; Zhao, Shuang; Han, Yifeng; Wu, Meixia; Liu, Sizhan; Tyson, Trevor A.; Croft, Mark; Li, Man-Rong (April 2020, Journal of Materials Chemistry C)

   null (Ed.)

   Exotic perovskites significantly enrich materials for multiferroic and magnetoelectric applications. However, their design and synthesis is a challenge due to the mostly required recipe conditions at extremely high pressure. Herein, we presented the Ca 2−x Mn x MnTaO 6 (0 ≤ x ≤ 1.0) solid solutions stabilized by chemical pressure assisted with intermediate physical pressure up to 7 GPa. The incorporation of Mn 2+ into the A-site neither drives any cationic ordering nor modifies the orthorhombic Pbnm structure, namely written as (Ca 1−x/2 Mn x/2 )(Mn 1/2 Ta 1/2 )O 3 with disordered A and B site cationic arrangements. The increment of x is accompanied by a ferromagnetic to antiferromagnetic transition around x = 0.2, which is attributed to the double-exchange interactions between A-site Mn 2+ and B-site Mn 3+ . Partial charge disproportionation of the B-site Mn 3+ into Mn 2+ and Mn 4+ occurs for x above 0.8 samples as manifested by X-ray spectrum and magnetic behaviors. The coexistence of B-site Mn 3+ (Jahn–Teller distortion ion) and B′-site Ta 5+ (second-order Jahn–Teller distortion ion) could be energetically responsible for the absence of A-site columnar ordering as observed in other quadruple perovskites with half of the A-sites occupied by small transition-metal cations. These exceptional findings indicate that exotic perovskites can be successfully stabilized at chemical and intermediate physical pressure, and the presence of Jahn–Teller distortion cations at the same lattice should be avoided to enable cationic ordering. 

   more » « less
4. Orthogonal, modular anion–cation and cation–anion self-assembly using pre-programmed anion binding sites

   https://doi.org/10.1039/D2SC05121D  

   Dhara, Ayan; Fadler, Rachel E.; Chen, Yusheng; Köttner, Laura A.; Van Craen, David; Carta, Veronica; Flood, Amar H. (March 2023, Chemical Science)

   Subcomponent self-assembly relies on cation coordination whereas the roles of anions often only emerge during the assembly process. When sites for anions are instead pre-programmed, they have the potential to be used as orthogonal elements to build up structure in a predictable and modular way. We explore this idea by combining cation (M + ) and anion (X − ) binding sites together and show the orthogonal and modular build up of structure in a multi-ion assembly. Cation binding is based on a ligand (L) made by subcomponent metal-imine chemistry (M + = Cu + , Au + ) while the site for anion binding (X − = BF 4 − , ClO 4 − ) derives from the inner cavity of cyanostar (CS) macrocycles. The two sites are connected by imine condensation between a pyridyl-aldehyde and an aniline-modified cyanostar. The target assembly [LM-CS-X-CS-ML], + generates two terminal metal complexation sites (LM and ML) with one central anion-bridging site (X) defined by cyanostar dimerization. We showcase modular assembly by isolating intermediates when the primary structure-directing ions are paired with weakly coordinating counter ions. Cation-directed (Cu + ) or anion-bridged (BF 4 − ) intermediates can be isolated along either cation–anion or anion–cation pathways. Different products can also be prepared in a modular way using Au + and ClO 4 − . This is also the first use of gold( i ) in subcomponent self-assembly. Pre-programmed cation and anion binding sites combine with judicious selection of spectator ions to provide modular noncovalent syntheses of multi-component architectures. 

   more » « less
5. X-ray emission spectroscopy: an effective route to extract site occupation of cations

   https://doi.org/10.1039/c8cp04628j  

   Bhargava, Anuj; Chen, Cindy Y.; Finkelstein, Kenneth D.; Ward, Matthew J.; Robinson, Richard D. (November 2018, Physical Chemistry Chemical Physics)

   Cation site occupation is an important determinant of materials properties, especially in a complex system with multiple cations such as in ternary spinels. Many methods for extracting the cation site information have been explored in the past, including analysis of spectra obtained through K-edge X-ray absorption spectroscopy (XAS). In this work, we measure the effectiveness of X-ray emission spectroscopy (XES) for determining the cation site occupation. As a test system we use spinel phase Co x Mn 3−x O 4 nanoparticles contaminated with CoO phases because Co and Mn can occupy all cation sites and the impurity simulates typical products of oxide syntheses. We take advantage of the spin and oxidation state sensitive Kβ 1,3 peak obtained using XES and demonstrate that XES is a powerful and reliable technique for determining site occupation in ternary spinel systems. Comparison between the extended X-ray absorption fine structure (EXAFS) and XES techniques reveals that XES provides not only the site occupation information as EXAFS, but also additional information on the oxidation states of the cations at each site. We show that the error for EXAFS can be as high as 35% which makes the results obtained ambiguous for certain stoichiometries, whereas for XES, the error determined is consistently smaller than 10%. Thus, we conclude that XES is a superior and a far more accurate method than XAS in extracting cation site occupation in spinel crystal structures. 

   more » « less