Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The ligand unwrapping/rewrapping pathway that exchanges metals in S-acetylated, hexacoordinate N2S2O2 complexes.

ABSTRACT: The effect of S-acetylation in MN2S2 complexes on metal exchange reactivity was examined in a series of MN2S2O2 complexes. While clean exchange processes do not occur for the MN2S2 derivatives where formation of S-bridged aggregates predominate, acetylation permits the metal exchange with hierarchy that follows the Irving-Williams series of stability for first row transition metals: Fe2+ < Co2+ < Ni2+ < Cu2+ > Zn2+. The rate determining step consistent with kinetic parameters depends on both M and M', supporting a mechanism of exchange that involves ligand unwrapping/rewrapping process as earlier defined by Margerum et al. for M(EDTA) systems. The enhanced metal exchange deriving from S-acetylation is of significance to probes and detection of cysteine-S metallo-proteins and metallo-enzyme active sites, and highlights a new role for S-acetylation.

SUBMITTER: Denny JA

PROVIDER: S-EPMC5954489 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The ligand unwrapping/rewrapping pathway that exchanges metals in S-acetylated, hexacoordinate N2S2O2 complexes.

Denny J A JA Foley W S WS Todd A D AD Darensbourg M Y MY

Chemical science 20150907 12

The effect of S-acetylation in MN2S2 complexes on metal exchange reactivity was examined in a series of MN2S2O2 complexes. While clean exchange processes do not occur for the MN2S2 derivatives where formation of S-bridged aggregates predominate, acetylation permits the metal exchange with hierarchy that follows the Irving-Williams series of stability for first row transition metals: Fe2+ < Co<su ...[more]

PMID: 29896341

Similar Datasets

Planar hexacoordinate gallium.

Project description:We report the first planar hexacoordinate gallium (phGa) center in the global minimum of the GaBe6Au6 + cluster which has a star-like D 6h geometry with 1A1g electronic state, possessing a central gallium atom encompassed by a Be6 hexagon and each Be-Be edge is further capped by an Au atom. The electronic delocalization resulting in double aromaticity (both σ and π) provides electronic stability in the planar form of the GaBe6Au6 + cluster. The high kinetic stability of the title cluster is also understood by Born-Oppenheimer molecular dynamics simulations. The energy decomposition analysis in combination with the 'natural orbitals for chemical valence' theory reveals that the bonding in the GaBe6Au6 + cluster is best expressed as the doublet Ga atom with 4s24p⊥ 1 electronic configuration forming an electron-sharing π bond with the doublet Be6Au6 + moiety followed by Ga(s)→[Be6Au6 +] σ-backdonation and two sets of Ga(p‖)←[Be6Au6 +] σ-donations.

| S-EPMC8612373 | biostudies-literature

σ-Aromatic MAl6S6 (M = Ni, Pd, Pt) Stars Containing Planar Hexacoordinate Transition Metals.

Project description:Hypercoordinate transition-metal species are mainly dominated by the 18-valence-electron (18ve) counting. Herein, we report ternary MAl6S6 (M = Ni, Pd, Pt) clusters with the planar hexacoordinate metal (phM) centers, which feature 16ve counting instead of the classic 18ve rule. These global-minimum clusters are established via unbiased global searches, followed by PBE0 and single-point CCSD(T) calculations. The phM MAl6 units are stabilized by six peripheral bridging S atoms in these star-like species. Chemical bonding analyses reveal that there are 10 delocalized electrons around the phM center, which can render the aromaticity according to the (4n + 2) Hückel rule. It is worth noting that adding an (or two) electron(s) to its π-type lowest unoccupied molecular orbital (LUMO) will make the system unstable.

| S-EPMC9920543 | biostudies-literature

Identification of metal species by ESI-MS/MS through release of free metals from the corresponding metal-ligand complexes.

Project description:Electrospray ionization-mass spectrometry (ESI-MS) is used to analyze metal species in a variety of samples. Here, we describe an application for identifying metal species by tandem mass spectrometry (ESI-MS/MS) with the release of free metals from the corresponding metal-ligand complexes. The MS/MS data were used to elucidate the possible fragmentation pathways of different metal-deoxymugineic acid (-DMA) and metal-nicotianamine (-NA) complexes and select the product ions with highest abundance that may be useful for quantitative multiple reaction monitoring. This method can be used for identifying different metal-ligand complexes, especially for metal species whose mass spectra peaks are clustered close together. Different metal-DMA/NA complexes were simultaneously identified under different physiological pH conditions with this method. We further demonstrated the application of the technique for different plant samples and with different MS instruments.

| S-EPMC4886218 | biostudies-literature

Structure and reactivity of hexacoordinate hemoglobins.

Project description:The heme prosthetic group in hemoglobins is most often attached to the globin through coordination of either one or two histidine side chains. Those proteins with one histidine coordinating the heme iron are called "pentacoordinate" hemoglobins, a group represented by red blood cell hemoglobin and most other oxygen transporters. Those with two histidines are called "hexacoordinate hemoglobins", which have broad representation among eukaryotes. Coordination of the second histidine in hexacoordinate Hbs is reversible, allowing for binding of exogenous ligands like oxygen, carbon monoxide, and nitric oxide. Research over the past several years has produced a fairly detailed picture of the structure and biochemistry of hexacoordinate hemoglobins from several species including neuroglobin and cytoglobin in animals, and the nonsymbiotic hemoglobins in plants. However, a clear understanding of the physiological functions of these proteins remains an elusive goal.

| S-EPMC4390088 | biostudies-literature

On the pathway of forming enzymatically productive ligand-protein complexes in lactate dehydrogenase.

Project description:We have carried out a series of studies on the binding of a substrate mimic to the enzyme lactate dehydrogenase (LDH) using advanced kinetic approaches, which begin to provide a molecular picture of the dynamics of ligand binding for this protein. Binding proceeds via a binding-competent subpopulation of the nonligated form of the protein (the LDH/NADH binary complex) to form a protein-ligand encounter complex. The work here describes the collapse of the encounter complex to form the catalytically competent Michaelis complex. Isotope-edited static Fourier transform infrared studies on the bound oxamate protein complex reveal two kinds of oxamate environments: 1), a major populated structure wherein all significant hydrogen-bonding patterns are formed at the active site between protein and bound ligand necessary for the catalytically productive Michaelis complex and 2), a minor structure in a configuration of the active site that is unfavorable to carry out catalyzed chemistry. This latter structure likely simulates a dead-end complex in the reaction mixture. Temperature jump isotope-edited transient infrared studies on the binding of oxamate with LDH/NADH suggest that the evolution of the encounter complex between LDH/NADH and oxamate collapses via a branched reaction pathway to form the major and minor bound species. The production of the catalytically competent protein-substrate complex has strong similarities to kinetic pathways found in two-state protein folding processes. Once the encounter complex is formed between LDH/NADH and substrate, the ternary protein-ligand complex appears to "fold" to form a compact productive complex in an all or nothing like fashion with all the important molecular interactions coming together at the same time.

| S-EPMC2440432 | biostudies-literature

Enantiomerically Pure Constrained Geometry Complexes of the Rare-Earth Metals Featuring a Dianionic N-Donor Functionalised Pentadienyl Ligand: Synthesis and Characterisation.

Project description:We report the preparation of enantiomerically pure constrained geometry complexes (cgc) of the rare-earth metals bearing a pentadienyl moiety (pdl) derived from the natural product (1R)-(-)-myrtenal. The potassium salt 1, [Kpdl*], was treated with ClSiMe2 NHtBu, and the resulting pentadiene 2 was deprotonated with the Schlosser-type base KOtPen/nBuLi (tPen=CMe2 (CH2 Me)) to yield the dipotassium salt [K2 (pdl*SiMe2 NtBu)] (3). However, 3 rearranges in THF solution to its isomer 3' by a 1,3-H shift, which elongates the bridge between the pdl and SiMe2 NtBu moieties by one CH2 unit. This is crucial for the successful formation of various monomeric C1 - or dimeric C2 -symmetric rare-earth cgc complexes with additional halide, tetraborohydride, amido and alkyl functionalities. All compounds have been extensively characterised by solid-state X-ray diffraction analysis, solution NMR spectroscopy and elemental analyses.

| S-EPMC7756846 | biostudies-literature

General stress response signalling: unwrapping transcription complexes by DNA relaxation via the sigma38 C-terminal domain.

Project description:Escherichia coli responds to stress by a combination of specific and general transcription signalling pathways. The general pathways typically require the master stress regulator sigma38 (rpoS). Here we show that the signalling from multiple stresses that relax DNA is processed by a non-conserved eight-amino-acid tail of the sigma 38 C-terminal domain. By contrast, responses to two stresses that accumulate potassium glutamate do not rely on this short tail, but still require the overall C-terminal domain. In vitro transcription and footprinting studies suggest that multiple stresses can target a poised RNA polymerase and activate it by unwrapping DNA from a nucleosome-like state, allowing the RNA polymerase to escape into productive mode. This transition can be accomplished by either the DNA relaxation or potassium glutamate accumulation that characterizes many stresses.

| S-EPMC2775543 | biostudies-literature

Crystallographic refinement of ligand complexes.

Project description:Model building and refinement of complexes between biomacromolecules and small molecules requires sensible starting coordinates as well as the specification of restraint sets for all but the most common non-macromolecular entities. Here, it is described why this is necessary, how it can be accomplished and what pitfalls need to be avoided in order to produce chemically plausible models of the low-molecular-weight entities. A number of programs, servers, databases and other resources that can be of assistance in the process are also discussed.

| S-EPMC2483469 | biostudies-literature

Structural insights into acetylated histone ligand recognition by the BDP1 bromodomain of Plasmodium falciparum.

Project description:Plasmodium falciparum requires a two-host system, moving between Anopheles mosquito and humans, to complete its life cycle. To overcome such dynamic growth conditions its histones undergo various post-translational modifications to regulate gene expression. The P. falciparum Bromodomain Protein 1 (PfBDP1) has been shown to interact with acetylated lysine modifications on histone H3 to regulate the expression of invasion-related genes. Here, we investigated the ability of the PfBDP1 bromodomain to interact with acetyllsyine modifications on additional core and variant histones. A crystal structure of the PfBDP1 bromodomain (PfBDP1-BRD) reveals it contains the conserved bromodomain fold, but our comparative analysis between the PfBDP1-BRD and human bromodomain families indicates it has a unique binding mechanism. Solution NMR spectroscopy and ITC binding assays carried out with acetylated histone ligands demonstrate that it preferentially recognizes tetra-acetylated histone H4, and we detected weaker interactions with multi-acetylated H2A.Z in addition to the previously reported interactions with acetylated histone H3. Our findings indicate PfBDP1 may play additional roles in the P. falciparum life cycle, and the distinctive features of its bromodomain binding pocket could be leveraged for the development of new therapeutic agents to help overcome the continuously evolving resistance of P. falciparum against currently available drugs.

| S-EPMC10093686 | biostudies-literature

Bare and ligand protected planar hexacoordinate silicon in SiSb3M3 + (M = Ca, Sr, Ba) clusters.

Project description:The occurrence of planar hexacoordination is very rare in main group elements. We report here a class of clusters containing a planar hexacoordinate silicon (phSi) atom with the formula SiSb3M3 + (M = Ca, Sr, Ba), which have D 3h (1A1') symmetry in their global minimum structure. The unique ability of heavier alkaline-earth atoms to use their vacant d atomic orbitals in bonding effectively stabilizes the peripheral ring and is responsible for covalent interaction with the Si center. Although the interaction between Si and Sb is significantly stronger than the Si-M one, sizable stabilization energies (-27.4 to -35.4 kcal mol-1) also originated from the combined electrostatic and covalent attraction between Si and M centers. The lighter homologues, SiE3M3 + (E = N, P, As; M = Ca, Sr, Ba) clusters, also possess similar D 3h symmetric structures as the global minima. However, the repulsive electrostatic interaction between Si and M dominates over covalent attraction making the Si-M contacts repulsive in nature. Most interestingly, the planarity of the phSi core and the attractive nature of all the six contacts of phSi are maintained in N-heterocyclic carbene (NHC) and benzene (Bz) bound SiSb3M3(NHC)6 + and SiSb3M3(Bz)6 + (M = Ca, Sr, Ba) complexes. Therefore, bare and ligand-protected SiSb3M3 + clusters are suitable candidates for gas-phase detection and large-scale synthesis, respectively.

| S-EPMC9278486 | biostudies-literature