Calcium in biological systems

On Local Structure Equilibration of Ca2+ in Solution by Ab Initio Molecular Dynamics

Analyzing the stable isotopic ratio of Ca offers valuable insights into a wide range of applications from climate reconstruction to bone cancer diagnosis and agricultural nutrient improvement. While the first hydration shell of Ca in solution is expected to play a major role in its fractionation properties, the coordination of Ca in water remains a subject of debate. In this work, Ca2+ in water has been modeled by means of ab initio molecular dynamics simulations using various exchange and correlation functionals and at different temperatures. Results show a significant effect of the functional on the average Ca2+ coordination, depending on its tendency to over- or understructure liquid water. The BLYP functional with Grimme-D2 correction was judged as the most accurate among those tested based on its accuracy to reproduce water structural and diffusion properties. Using this functional, the effect of temperature has been systematically investigated, focusing on means to limit the uncertainty in our assessments of the average coordination of Ca2+ ions by (1) estimating the number of water exchanges in the simulations and (2) implementing a statistical approach based on Markov chains. The findings indicate, especially, that our simulations at 300, 350, and 400 K do not yield converged results due to potential equilibration problems. These observations impose substantial constraints on the trustworthiness of numerous estimates in the existing literature that depend on trajectories with insufficient exchanges. We estimate Ca2+ coordination values of 6.8 ± 0.1, 6.8 ± 0.1, 6.7 ± 0.2, and 6.7 ± 0.2 at 600, 550, 500, and 450 K respectively. At lower temperatures (300, 350, and 400 K), while obtaining definitive values for Ca2+ coordination remains challenging, our research does indicate a potential temperature-related influence on coordination with an average Ca2+ coordination at 300 K as low as 6.2.

Be2+ Causes Hypersensitivity but Mg2+ and Ca2+ Do Not─Favorable Metal Coordination Is the Key for Differential Allosteric Modulation and Binding Affinities

Although the ion selectivity of metalloproteins has been well established, selective metal antigen recognition by immunoproteins remains elusive. One such case is the recognition of the Be2+ ion against its heavier congeners, Mg2+ and Ca2+, by the human leukocyte antigen immunoprotein (HLA-DP2), leading to immunotoxicity. Integrating with our previous mechanistic study on Be2+ toxicity, herein, we have explored the basis of characteristic nontoxicity of Mg2+ and Ca2+ ions despite their in vivo abundance. The ion binding cleft of the HLA-DP2-peptide complex is composed of four acidic residues, p4D and p7E from the peptide and β26E and β69E from the protein. While the tetrahedral coordination site of the smaller Be2+ ion is located deep inside the cavity, hexa- to octa-coordination sites of Mg2+ and Ca2+ ions are located closer to the protein surface. The intrinsic high coordination number of Mg2+/Ca2+ ions induces allosteric modifications on the HLA-DP2_M2 surface, which are atypical for TCR recognition. Furthermore, the lower binding energy of larger Mg2+ and Ca2+ ions with the cavity residues can be correlated to the lower charge density and reduced covalent bonding nature as compared to those of the smaller Be2+ ion. In short, weak binding of Mg2+ and Ca2+ ions and the unfavorable allosteric surface modifications are probably the major determinants for the absence of Mg2+/Ca2+ ion-mediated hypersensitivity in humans.

Genetically Encoded Fluorescence/Bioluminescence Bimodal Indicators for Ca2+ Imaging

Fluorescent and bioluminescent genetically encoded Ca²⁺ indicators (GECIs) are an indispensable tool for monitoring Ca²⁺ dynamics in numerous cellular events. Although fluorescent GECIs have a high spatiotemporal resolution, their application is often confined to short-term imaging due to the external illumination that causes phototoxicity and autofluorescence from specimens. Bioluminescent GECIs overcome these pitfalls with enhanced compatibility to optogenetic manipulation and photophysiological processes; however, they are compromised for spatiotemporal resolution. Therefore, there has been a push toward the use of Ca²⁺ indicators that possess the advantages of both fluorescent and bioluminescent GECI for a wide range of applications. To address this, we developed a high-affinity bimodal GECI, GLICO, using a single fluorescent protein-based GECI combined with a split luciferase. Through this novel design, the fusion protein becomes bimodal and possesses Ca²⁺ sensing properties similar to those of its fluorescent ancestor and confers bioluminescence-based Ca²⁺ imaging. GLICO in bioluminescence mode has the highest dynamic range (2200%) of all bioluminescent GECIs. We demonstrated the performance of GLICO in studying cytosolic Ca²⁺ dynamics in different cultured cells in each mode. With the purpose of Ca²⁺ imaging in high Ca²⁺ content organelle, we also created a low-affinity variant, ReBLICO and performed Ca²⁺ imaging of the ER in both fluorescence and bioluminescence modes. The ability to switch between fluorescence and bioluminescence modes with a single indicator would benefit transgenic applications by presenting an opportunity for a wide range of live Ca²⁺ imaging in physiological and pathophysiological conditions.

Bioluminescent Low-Affinity Ca2+ Indicator for ER with Multicolor Calcium Imaging in Single Living Cells

The sarco/endoplasmic reticulum (SR/ER) is the foremost intercellular Ca²⁺ store (at submillimolar concentrations), playing a crucial role in controlling intracellular Ca²⁺ levels. For the investigation of SR/ER Ca²⁺ dynamics in cells, fluorescent protein-based genetically encoded calcium indicators (GECIs) with low Ca²⁺ affinity have been used. Recently, bioluminescent protein-based GECIs with high brightness have been reported to counter the constraints of fluorescence imaging, such as phototoxicity. However, their Ca²⁺ affinity is high and limited for imaging in the cytosol, nucleus, or mitochondria. In this study, we developed a novel cyan color, low-affinity ( K_d = 110 μM) intensiometric bioluminescent GECI, which enables monitoring of the Ca²⁺ dynamics in the ER of HeLa cells and the SR of C2C12-derived myotubes. To facilitate the broad concentration range of Ca²⁺ in cellular organelles, we additionally developed an intermediate affinity ( K_d = 18 μM), orange color, and bioluminescent GECI, which enables monitoring of Ca²⁺ dynamics in the mitochondria of HeLa cells. With these indicators, in conjunction with an existing high-affinity, green, bioluminescent GECI, we succeeded in multicolor bioluminescent Ca²⁺ imaging in three distinct organelles (nuclei, mitochondria, and ER) simultaneously. The multicolor, live, bioluminescent Ca²⁺ imaging demonstrated here can be used to stably reveal the ER Ca²⁺ homeostasis and cooperative Ca²⁺ regulation among organelles. This will lead to the further understanding of Ca²⁺-related physiological functions and pathophysiological mechanisms.

Crystal structures of [SbF6]− salts of di- and tetrahydrated Ag +, tetrahydrated Pd2 + and hexahydrated Cd2 + cations

The [Ag(H2O)2]SbF6, is triclinic, P1̅ (No. 2), with a=6.6419(3) Å, b=7.6327(3) Å, c=11.1338(3) Å, α=95.492(3)°, β=96.994(3)°, γ=113.535(4)°, V=507.13(4) Å3 at 150 K, and Z=3. There are two crystallographically non-equivalent Ag+ cations. The Ag1 is coordinated by two water molecules with Ag–OH2 distances equal to 2.271(2) Å forming in that way a discrete linear [Ag(H2O)2]+ cation. Additionaly, it forms two short Ag···F contacts (2.630(2) Å), resulting in AgO2F2 plaquette, and four long ones (2×3.001(2) Å and 2×3.095(2) Å) with fluorine atoms located below and above the AgO2F2 plaquette. The H2O molecules bridge Ag2 atoms into {–[Ag(μ-OH2)2]–}n infinite chains, with Ag–O distances of 2.367(2)–2.466(2) Å. The [Pd(H2O)4](SbF6)2·4H2O is monoclinic, P2 1 /a (No.14), with a=8.172(2) Å, b=13.202(3) Å, c=8.188(3) Å, β=115.10(1)o, V=799.9(4) Å3 at 200 K, and Z=2. Its crystal structure can be described as an alternation of layers of [Pd(H2O)4]2+ cations (interconnected by H2O molecules) and [SbF6]− anions. It represents the first example where [Pd(H2O)4]2+ has been structurally determined in the solid state. Four oxygen atoms provided by H2O molecules are in almost ideal square-planar arrangement with Pd–O bond lengths 2×2.004(5) Å and 2×2.022(6) Å. The [Cd(H2O)6](SbF6)2, is orthorhombic, Pnnm (No.58), with a=5.5331(2) Å, b=14.5206(4) Å, c=8.9051(3) Å, V=715.47(4) Å3 at 200 K, and Z=2. It consists of [Cd(H2O)6]2+ cations and [SbF6]− anions.