The role of hydrated divalent metal ions in the bridging of two anionic groups. An ab initio quantum chemical and molecular mechanics study of dimethyl phosphate and formate bridged by calcium and magnesium ions

Ab initio quantum chemical (Gaussian82) and molecular mechanics (AMBER2.0) computational techniques are employed to investigate the interaction of two anions (formate an dimethylphosphate) and a central divalent metal cation (magnesium or calcium). These systems are models for the essential GDP binding unit of the G-proteins (e.g., EF-Tu or the ras oncogene proteins) and for protein/phospholipid interactions, both of which are mediated by divalent metal cations. Various levels of hydration are utilized to examine coordination of differences between magnesium and calcium ions. Two different orientations of formate and dimethyl phosphate in direct ion contact with a magnesium ion and two waters of hydration were energy minimized with both quantum and molecular mechanics techniques. The structures and energy differences between the two orientations determined by either of the computational techniques are similar. Magnesium ion has a strong propensity to assume six coordination whereas calcium ion preferentially assumes a coordination greater than six. Likewise, water molecules attached to magnesium ion are held more rigidly than those of calcium ion, thus calcium ion is more accommodating in the exchange of water for negative ligands.     

The Role of Hydrated Divalent Metal Ions in the Bridging of Two Anionic Groups. An ab initio Quantum Chemical and Molecular Mechanics Study of Dimethyl Phosphate and Formate Bridged by Calcium and Magnesium Ions

Abstract

Ab initio quantum chemical (Gaussian82) and molecular mechanics (AMBER2.0) computational techniques are employed to investigate the interaction of twoanions (formate and dimethyl phosphate) and a central divalent metal cation (magnesium or calcium). These systems are models for the essential GDP binding unit of the G-proteins (e.g., EF-Tu or the ras oncogene proteins) and for protein/phospholipid interactions, both of which are mediated by divalent metal cations. Various levels of hydration are utilized to examine coordination of differences between magnesium and calcium ions. Two different orientations of formate and dimethyl phosphate in direct ion contact with a magnesium ion and two waters of hydration were energy minimized with both quantum and molecular mechanics techniques. The structures and energy differences between the two orientations determined by either of the computational techniques are similar. Magnesium ion has a strong propensity to assume six coordination whereas calcium ion preferentially assumes a coordination greater than six. Likewise, water molecules attached to magnesium ion are held more rigidly than those to calcium ion, thus calcium ion is more accommodating in the exchange of water for negative ligands.     

Delay of intracellular calcium transients using a calcium chelator: application to high-throughput screening of the capsaicin receptor ion channel and G-protein-coupled receptors.

Whole-cell functional assays are often used for high-throughput screening (HTS) of molecular targets such as ion channels and G-protein-coupled receptors. A common method for assaying the activity of these membrane proteins is to measure the change in intracellular calcium concentration upon receptor stimulation. These changes in calcium concentration are typically transient and therefore not readily adapted to high-density plate formats used in HTS instruments. We have demonstrated that an intracellular calcium chelator, BAPTA, was able to delay by 5- to 20-fold and extend for several minutes the observed calcium signals initiated by extracellular calcium influx or release of calcium from intracellular stores. As examples, we used cells expressing a calcium-permeable ion channel, vanilloid receptor type 1 (the capsaicin receptor), and two G-protein-coupled receptors. These receptor-mediated increases in intracellular calcium concentration were measured by both fluorescence-based and luminescence-based detection methods. The use of an intracellular calcium chelator to delay calcium signaling should have wide application since it allows the measurement of the functional activity of any cellular receptor that signals through calcium. With this procedure, calcium fluorescence and luminescence whole-cell functional assays may be performed with standard laboratory pipetting and detection systems.     

The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium-loaded state

We determine and compare the crystal structure of two proteases belonging to the subtilisin superfamily: S41, a cold-adapted serine protease produced by Antarctic bacilli, at 1.4 A resolution and Sph, a mesophilic serine protease produced by Bacillus sphaericus, at 0.8 A resolution. The purpose of this comparison was to find out whether multiple calcium ion binding is a molecular factor responsible for the adaptation of S41 to extreme low temperatures. We find that these two subtilisins have the same subtilisin fold with a root mean square between the two structures of 0.54 A. The final models for S41 and Sph include a calcium-loaded state of five ions bound to each of these two subtilisin molecules. None of these calcium-binding sites correlate with the high affinity known binding site (site A) found for other subtilisins. Structural analysis of the five calcium-binding sites found in these two crystal structures indicate that three of the binding sites have two side chains of an acidic residue coordinating the calcium ion, whereas the other two binding sites have either a main-chain carbonyl, or only one acidic residue side chain coordinating the calcium ion. Thus, we conclude that three of the sites are of high affinity toward calcium ions, whereas the other two are of low affinity. Because Sph is a mesophilic subtilisin and S41 is a psychrophilic subtilisin, but both crystal structures were found to bind five calcium ions, we suggest that multiple calcium ion binding is not responsible for the adaptation of S41 to low temperatures.     

Multiple forms of Ca-activated protease from rat brain and muscle

Three Ca-dependent proteases have been identified in rat brain and skeletal muscle using ion exchange, gel filtration, and substrate affinity chromatography. A high degree of homology exists among three enzymes from different sources. Both the high molecular weight protease (154,000) and lower molecular weight protease (96,000) show high affinity for calcium while the third protease (76,000) had low affinity for calcium. Transformation among the three enzymes was calcium-induced and the process was unidirectional, generating a lower molecular weight form with decreased affinity for calcium. The protease with low affinity for calcium was susceptible to calcium-induced inactivation by autocatalysis. Immunologically the three proteases were equivalent, if not identical, and the brain and muscle proteases cross-react. All three proteases degraded neurofilament proteins; however, the protease with low affinity for calcium had 3 to 6 times higher specific activity. It is suggested that the high molecular weight enzyme (154,000) may be the native form of the Ca-dependent protease present in vivo.     

Energy-dependent cell cohesion in myxobacteria

Cohesion in the myxobacterium Stigmatella aurantiaca was characterized. Two classes of cohesion were revealed, termed class A and class B. Class A cohesion is a characteristic of vegetative cells grown in tryptone or casitone (Difco Laboratories, Detroit, Mich.), whereas class B cohesion requires the addition of calcium ion for induction. Class A cohesion occurs in the presence of any cation and is temperature independent. Class B cohesion requires the presence of a cation in the calcium group and is energy dependent. We conclude that S. aurantiaca responds to calcium ion by synthesizing the molecular components of a system of cell cohesion (class B) and that the functioning of this system requires the expenditure of metabolic energy.     

CaCCs通道钙离子依赖性机制的研究进展

钙激活氯离子通道(Ca CCs)是一种广泛存在的氯离子通道,参与众多生理功能,如:上皮细胞的离子分泌、嗅觉传导以及平滑肌收缩等。由于通常情况下很难将Ca CCs介导的电流和钙离子依赖性阳离子流以及非钙离子依赖性氯离子流分开,因此其钙离子依赖性机制的研究远远滞后于其他离子通道。本文综述了最新报道的Ca CCs分子基础跨膜蛋白TMEM16A的发现和确立、结构特点、钙离子结合位点、其电流发生机制,及其相关生理作用以及病理和药理功能的热点问题,并展望该领域的研究发展趋势。     

Structure of acidic phospholipase A2 for the venom of Agkistrodon halys blomhoffii at 2.8 A resolution.

The crystal structure of acidic phospholipase A2 from the venom of Agkistrodon halys blomhoffii has been determined by molecular replacement methods based on the known structure of Crotalus atrox PLA2, a same group II enzyme. The overall structures, except the calcium-binding regions, are very similar to each other. A calcium ion is pentagonally ligated to two carboxylate oxygen atoms of Asp-49 and each carbonyl oxygen atoms of Tyr-28, Gly-30 and Ala-31. A reason why the former enzyme functions as monomeric form, while the latter one does as dimer, could be presumed by the structural comparison of these calcium-binding regions. Although Gly-32 is usually participated as a ligand in the coordination with calcium ion in group I PLA2, it is characteristically replaced to Ala-31 in the present structure, and thus the coordination geometry of calcium ion is rather different from the usually observed one.     

Biochemical analysis of L-type calcium channels from skeletal and cardiac muscle

The development of specific pharmacological agents that modulate different types of ion channels has prompted an extensive effort to elucidate the molecular structure of these important molecules. The calcium channel blockers that specifically modulate the L-type calcium channel activity have aided in the purification and reconstitution of this channel from skeletal muscle transverse tubules. The L-type calcium channel from skeletal muscle is composed of five subunits designated alpha 1, alpha 2, beta, gamma, and sigma. The alpha 1-subunit is the pore-forming polypeptide and contains the ligand binding and phosphorylation sites through which channel activity can be modulated. The role of the other subunits in channel function remains to be studied. The calcium channel components have also been partially purified from cardiac muscle. The channel consists of at least three subunits that have properties related to the subunits of the calcium channel from skeletal muscle. A core polypeptide that can form a channel and contains ligand binding and phosphorylation sites has been identified in cardiac preparations. Here we summarize recent biochemical and molecular studies describing the structural features of these important ion channels.     

The calibration and use of a calcium ion-specific electrode for kinetic studies of mitochondrial calcium transport.

A calcium ion-specific electrode has been used to study calcium transport by isolated,hepatic mitochondria. The methodology used requires only a sensitive pH meter operated in the millivolt mode with the electrode. Free calcium ion concentrations may be followed continuously. Using incubation conditions which cause release of intramitochondrial calcium, the calcium electrode system may also be used to determine total. intramitochondrial calcium. Techniques for the calibration of the electrode response are discussed. Free calcium ion concentrations have been calculated from total calcium concentrations and the association constants for the binding species present in the assay medium. The observation that the electrode response is linear to submicromolar concentrations allows calculation of a linear least-squares fit of millivolt reading to computed free calcium ion concentration. A computer program written in BASIC for these computations is included in Appendix material. The half-maximal rate constant for mitochondrial calcium uptake has been found to occur at a free calcium ion concentration of 6.5 μm. The interaction or Hill coefficient for the process is 2.3, indicating positive cooperativity.     

Interaction of human calpains I and II with high molecular weight and low molecular weight kininogens and their heavy chain: mechanism of interaction and the role of divalent cations

Calpain I prepared from human erythrocytes was half-maximally and maximally activated at 23 and 35 microM calcium ion, and two preparations of calpain II from human liver and kidney were half-maximally activated at 340 and 220 microM calcium ion and maximally activated at 900 microM calcium ion, respectively. High molecular weight (HMW) and low molecular weight (LMW) kininogens isolated from human plasma and the heavy chain prepared from these proteins inhibited calpain I as well as calpain II. The molar ratios of calpains to HMW kininogen to give complete inhibition of calpains were 1.4 for calpain I and 2.0 for calpain II, and those of calpains to heavy chain were 0.40-0.66 for calpain I and 0.85 for calpain II. LMW kininogen did not completely inhibit the calpains even with an excess amount of kininogen. The apparent binding ratio of calpain to HMW kininogen estimated from the disc gel electrophoretic analysis, however, was found to be 2:1, whereas those of calpain to LMW kininogen and of calpain to heavy chain were found to be 1:1. Calpains and kininogens failed to form complexes in the absence of calcium ion. In the presence of calcium ion, however, they formed the complexes, which were dissociable by the addition of ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid. The minimum concentrations of calcium ion required to induce complex formation between calpain I and kininogens and calpain II and kininogens were 70 and 100 microM, respectively. Some other divalent cations such as Mn2+, Sr2+, and Ba2+ were also able to induce the complex formation between calpains and kininogens.(ABSTRACT TRUNCATED AT 250 WORDS)     

Properties, intracellular localization, and stage-specific expression of membrane-bound beta-glucosidase, BglM1, from Physarum polycephalum

Physarum polycephalum expresses a membrane-bound beta-glucosidase (BglM1) with a molecular mass of 130 kDa. The primary structure of BglM1 consists of a glycosyl hydrolase family 3 domain at an amino-terminal domain and a carboxyl-terminal region without homology to the sequence of known glycosidases. The latter region contains two calx-beta motifs known as Ca(2+)-binding sites; an RGD sequence, which is known to be a cell attachment sequence; and a transmembrane region. The molecular mass calculated from the amino acid sequence is 130 kDa, but that in the crude extract was estimated by SDS-PAGE to be 230 kDa, and decreased to 130 kDa during purification. However, when BglM1 was purified in the presence of calcium ion, the molecular mass remained 230 kDa. The biochemical characteristics of the 130- and 230-kDa BglM1 forms were analyzed: differences were found in the kinetic data for some substrates specific for both these enzymes; however, no difference was found in their intrinsic characteristics such as optimum pH and temperature. In addition, the molecular mass of native BglM1 with a calcium ion was estimated to be 1,000 kDa or larger by gel filtration. These results suggest that the calcium ion influences the conformation of BglM1. The evidence that BglM1 localizes on the plasma membrane of plasmodia was confirmed using immunofluorescence microscopy. Although Physarum BglM1 was expressed in microplasmodia and plasmodia, little expression was detected in other stages. BglM1 may have some function only in multinuclear cells.     

Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites

The crystal structure of a calcium-free alpha-amylase (AmyK38) from Bacillus sp. strain KSM-K38, which resists chelating reagents and chemical oxidants, has been determined by the molecular replacement method and refined to a crystallographic R-factor of 19.9% (R-free of 23.2%) at 2.13-A resolution. The main chain folding of AmyK38 is almost homologous to that of Bacillus licheniformis alpha-amylase. However, neither a highly conserved calcium ion, which is located at the interface between domains A and B, nor any other calcium ions appear to exist in the AmyK38 molecule, although three sodium ions were found, one of which is located at the position corresponding to that of a highly conserved calcium ion of other alpha-amylases. The existence of these sodium ions was crystallographically confirmed by the structures of three metal-exchanged and mutated enzymes. This is the first case in which the structure of the calcium-free alpha-amylase has been determined by crystallography, and it was suggested that these sodium ions, instead of calcium ions, are used to retain the structure and function of AmyK38.     

Atomistic modeling and molecular dynamics analysis of human CaV1.2 channel using external electric field and ion pulling simulations

BackgroundHuman Ca_V1.2 (hCav1.2), a calcium selective voltage-gated channel, plays important roles in normal cardiac and neuronal functions. Calcium influx and gating mechanisms leading to the activation of hCa_V1.2 are critical for its functionalities. Lack of an experimentally resolved structure of hCa_V1.2 remains a significant impediment in molecular-level understanding of this channel. This work focuses on building atomistic hCa_V1.2 model and studying calcium influx using computational approaches.MethodsWe employed homology modeling and molecular dynamics (MD) to build the structure of hCa_V1.2. Subsequently, we employed steered molecular dynamics (SMD) to understand calcium ion permeation in hCa_V1.2.ResultsWe report a comprehensive three-dimensional model of a closed state hCa_V1.2 refined under physiological membrane-bound conditions using MD simulations. Our SMD simulations on the model revealed four important barriers for ion permeation: this includes three calcium binding sites formed by the EEEE- and TTTT- rings within the selectivity filter region and a large barrier rendered by the hydrophobic internal gate. Our results also revealed that the first hydration shell of calcium remained intact throughout the simulations, thus playing an important role in ion permeation in hCa_V1.2.ConclusionsOur results have provided some important mechanistic insights into the structure, dynamics and ion permeation in hCa_V1.2. The significant barriers for ion permeation formed by the four phenylalanine residues at the internal gate region suggest that this site is important for channel activation.     

Imaging of Calcium Channels During Polarity Induction in Plant Cells

Understanding the molecular basis of polarity induction in plant cells is a research aspect that extends from signal perception and transduction to morphogenesis. A gradient of cytoplasmic ion fluxes generated through ion channels plays a crucial role in subsequent events leading to polar growth. Convincing evidence is now available implicating temporal and spatial distribution of Ca²⁺ in cytoplasm, generated by localized activity of calcium channels, as the early biochemical events associated with polarity induction. Ion channel antagonists are common tools for studying ion channel structure and function. Coupled with a fluorescent dyes, calcium channel antagonists (phenylalkylamine and dihydropyridine), have been used to localize L-type calcium channels. Additionally, the advent of Confocal Laser Scanning Microscopy has made possible the visualization of Ca²⁺ channels in plant cells. Persisting problems of dye loading and their cellular compartmentation have been addressed by developing a variety of experimental protocols. Present article highlights the current state of our understanding of these concepts, methodologies and their applications in different aspects of plant development.     

Crystal structures of the apo- and holomutant human lysozymes with an introduced Ca2+ binding site

The three-dimensional structures of apo- and holomutant human lysozymes (D86/92 lysozyme), in which a calcium binding site was designed and created for enhancing molecular stability by replacing both Gln86 and Ala92 with aspartic acids, were refined at 1.8-A resolution by x-ray crystallography. The overall structures and crystallographic thermal factors of all three proteins, the apo-, holo-D86/92, and the wild-type human lysozymes, were essentially identical; these results showed that the introduction of the calcium binding site did not affect either the overall structure or molecular rigidity of the proteins. However, structure analyses of the apo-D86/92 lysozyme revealed that the mutations affected the side chain conformation of residue 86 and hydrogen networks between the protein and the internal solvent molecules. In the structure of the holo-D86/92 lysozyme, seven oxygen ligands formed a slightly distorted pentagonal bipyramid around the calcium ion, indicating that the coordination around the calcium ion was quite similar to that in baboon alpha-lactalbumin. The pentagonal bipyramid coordination could be one of the most widely found and appropriate calcium binding schemes in proteins.     

The role of calcium ions in freezing injuries of winter oilseed rape leaves. Effects of calcium channel blockers and mimesis by calcium ionophore

Calcium ionophore A23187 allowing for a calcium ion influx from an apoplast to a cytoplasm, mimicked symptoms of the frost-induced injuries in winter oilseed rape leaves, as estimated by the conductivity method. Both calcium ionophore and freezing treatment induced degradation of phosphatidylcholine. On the other hand lanthanum and gadolinum ions as well as verapamil, the inhibitors of calcium ion channels, decreased the degree of the frost-induced injuries. Lanthanum ions prevented the frost-induced degradation of PC. It is proposed that freezing alters the functioning of calcium ion channels which results in calcium ion influx into a cytosol. This in turn may lead to a degradation of cell membranes.     

Expression of the ipomoelin gene from sweet potato is regulated by dephosphorylated proteins, calcium ion and ethylene

A wound‐inducible cDNA, ipomoelin (IPO) was isolated from the subtraction library of sweet potato (Ipomoea batatas cv. Tainung 57) and used as a molecular probe to investigate the transduction pathway of wounding signal within plant cells. Following mechanical wounding of the leaves of sweet potato, IPO mRNA accumulation peaked at 6 h and then continuously declined. However, IPO gene expression in the apical unwounded leaves began at 6 h after wounding and continued for a further 10 h. Besides mechanical wounding, methyl jasmonate (MeJA) was identified as a signal transducer leading to the accumulation of IPO mRNA. Treatment with salicylic acid reduced the production of IPO mRNA, further supporting the involvement of the octadecanoid pathway in the signal transduction of wounding in sweet potato. In addition, ethylene was involved in the signal pathway and induced the expression of the IPO gene. Furthermore, the application of okadaic acid, a protein phosphatase inhibitor, blocked the accumulation of IPO mRNA induced by MeJA or ethylene, indicating that activation of the IPO gene by both MeJA and ethylene was via dephosphorylated proteins. The presence of a calcium ion chelator or channel blockers also inhibited the expression of the IPO gene after wounding. However, investigation by confocal scanning microscopy further pointed out that mechanical wounding rather than the application of MeJA induced the accumulation of the calcium ion. These results may indicate that the calcium ion is also involved in the activation of IPO mRNA. In addition, wounding signals the accumulation of calcium ion first and then stimulates the biosynthesis of MeJA in sweet potato. Hence, the reaction sequence of signal transducers, including the calcium ion, MeJA and protein kinase/phosphatase, in the wounding signalling pathway of sweet potato is suggested in this report.     

Calcium-binding protein in bull seminal vesicle secretion and seminal plasma.

A protein which showed high affinity for calcium ions was isolated from bull seminal vesicle secretion and seminal plasma. Its calcium-binding activity depended on the ionic strength and pH of the medium. The dissociation constant was 7-7 X 10(-7) M and there were 14 binding sites per protein molecule. The molecular weight of calcium-binding protein from bull seminal vesicle secretion, estimated by the gel filtration method, was 110,000. The protein may be involved in the regulation of the calcium ion level in seminal plasma.     

Structural and mutational analyses of Drp35 from Staphylococcus aureus: a possible mechanism for its lactonase activity

Drp35 is a protein induced by cell wall-affecting antibiotics or detergents; it possesses calcium-dependent lactonase activity. To determine the molecular basis of the lactonase activity, we first solved the crystal structures of Drp35 with and without Ca(2+); these showed that the molecule has a six-bladed beta-propeller structure with two calcium ions bound at the center of the beta-propeller and surface region. Mutational analyses of evolutionarily conserved residues revealed that the central calcium-binding site is essential for the enzymatic activity of Drp35. Substitution of some other amino acid residues for the calcium-binding residues demonstrated the critical contributions of Glu(48), Asp(138), and Asp(236) to the enzymatic activity. Differential scanning calorimetric analysis revealed that the loss of activity of E48Q and D236N, but not D138N, was attributed to their inability to hold the calcium ion. Further structural analysis of the D138N mutant indicates that it lacks a water molecule bound to the calcium ion rather than the calcium ion itself. Based on these observations and structural information, a possible catalytic mechanism in which the calcium ion and its binding residues play direct roles was proposed for the lactonase activity of Drp35.