Browse
Submit Data
Databases
API
Help

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Time-Resolved Studies of Ytterbium Distribution at Interfacial Surfaces of Ferritin-like Dps Protein Demonstrate Metal Uptake and Storage Pathways.

ABSTRACT: Cage-shaped protein (CSP) complexes are frequently used in bionanotechnology, and they have a variety of different architectures and sizes. The smallest cage-shaped protein, Dps (DNA binding protein from starved cells), can naturally form iron oxide biominerals in a multistep process of ion attraction, translocation, oxidation, and nucleation. The structural basis of this biomineralization mechanism is still unclear. The aim of this paper is to further develop understanding of this topic. Time-resolved metal translocation of Yb³⁺ ions has been investigated on Dps surfaces using X-ray crystallography. The results reveal that the soak time of protein crystals with Yb³⁺ ions strongly affects metal positions during metal translocation, in particular, around and inside the ion translocation pore. We have trapped a dynamic state with ongoing translocation events and compared this to a static state, which is reached when the cavity of Dps is entirely filled by metal ions and translocation is therefore blocked. By comparison with La³⁺ and Co²⁺ datasets, the time-dependence together with the coordination sphere chemistry primarily determine metal-protein interactions. Our data can allow structure-based protein engineering to generate CSPs for the production of tailored nanoparticles.

SUBMITTER: Zeth K

PROVIDER: S-EPMC8389677 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the DNA-Mediated Oxidation of Dps, A Bacterial Ferritin.

Project description:Dps proteins are bacterial ferritins that protect DNA from oxidative stress and have been implicated in bacterial survival and virulence. In addition to direct oxidation of the Dps iron sites by diffusing oxidants, oxidation from a distance via DNA charge transport (CT), where electrons and electron holes are rapidly transported through the base-pair ?-stack, could represent an efficient DNA protection mechanism utilized by Dps. Here, we spectroscopically characterize the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation using an intercalating ruthenium photooxidant and the flash-quench technique. Upon irradiation with poly(dGdC)2, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)2 is substituted with poly(dAdT)2, the yield of Dps oxidation is decreased significantly, consistent with guanine radical intermediates facilitating Dps oxidation. We have also explored possible protein electron transfer (ET) intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the iron-binding ferroxidase site (W52 in E. coli Dps). In EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, a W52A Dps mutant was significantly deficient compared to WT Dps in forming the characteristic EPR signal at g = 4.3, consistent with W52 acting as an ET hopping intermediate. This effect is mirrored in vivo in E. coli survival in response to hydrogen peroxide, where mutation of W52 leads to decreased survival under oxidative stress.

| S-EPMC5014645 | biostudies-literature

DNA protection by the bacterial ferritin Dps via DNA charge transport.

Project description:Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. Here we examine the mechanism of E. coli Dps protection of DNA, specifically whether this DNA-binding protein can utilize DNA charge transport through the base pair π-stack to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate DNA damage localized to guanine repeats, the sites of lowest potential in DNA. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps, significantly attenuates the yield of oxidative DNA damage. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA charge transport may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.

| S-EPMC3899832 | biostudies-literature

Nanoscale interfacial gradients formed by the reactive uptake of OH radicals onto viscous aerosol surfaces.

Project description:A key but poorly understood chemical process is how gas phase uptake is governed by the relative mobility of molecules at an interface of an atmospheric aerosol. Citric acid (CA), a model system for oxygenated organic aerosol, is used to examine how changes in viscosity, due to changing water content, govern the reactive uptake of gas phase hydroxyl radicals (OH). By comparing the reaction kinetics measured when probing the outer aerosol surface layers with measurements of the bulk particle composition, the effective OH reaction probability is observed to be a complex and non-linear function of the relative humidity (RH). At RH < 50%, the reactive decay of CA is controlled by the viscosity of the particle, where the depletion of CA and the formation of reaction products occurs over a narrow region near the aerosol interface, on the order of 8 nm at 20% RH. At RH = 50% the reaction zone increases to the particle dimensions (i.e. ?50 nm) and at RH > 50%, the aerosol becomes aqueous and well-mixed on the timescale of the heterogeneous reaction. These results imply that in the atmosphere, the formation and dissipation of interfacial chemical gradients could be significant in viscous and semisolid aerosol and play important roles altering gas-particle partitioning and aging mechanisms (i.e. bulk vs. interface).

| S-EPMC5947524 | biostudies-other

Icephobic Surfaces Induced by Interfacial Nonfrozen Water.

Project description:It is known that smooth, hydrophobic solid surfaces exhibit low ice adhesion values, which have been shown to approach a lower ice adhesion strength limit (∼150 kPa) defined by the water receding contact angle. To overcome this limit, we have designed self-lubricating icephobic coatings by blending polydimethylsiloxane (PDMS)-poly(ethylene glycol) (PEG) amphiphilic copolymers into a polymer matrix. Such coatings provide low ice adhesion strength values (∼50 kPa) that can substantially reduce the lower bound of the ice adhesion strength achieved previously on smooth, hydrophobic solid surfaces. Different molecular mechanisms are responsible for the low ice adhesion strength attained by these two approaches. For the smooth hydrophobic surfaces, an increased water depletion layer thickness at the interface weakens the van der Waals' interactions between the ice and the polymeric substrate. For the self-lubricating icephobic coatings, the PEG component of the amphiphilic copolymer is capable of strongly hydrogen bonding with water molecules. The surface hydrogen-bonded water molecules do not freeze, even at substantial levels of subcooling, and therefore serve as a self-lubricating interfacial liquid-like layer that helps to reduce the adhesion strength of ice to the surface. The existence of nonfrozen water molecules at the ice-solid interface is confirmed by solid-state nuclear magnetic resonance (NMR) spectroscopy.

| S-EPMC6911363 | biostudies-literature

Electrodeposited surfaces with reversibly switching interfacial properties.

Project description:Engineered surfaces with reversibly switching interfacial properties, such as wettability and liquid repellency, are highly desirable in diverse application fields but are rare. We have developed a general concept to prepare metallic porous surfaces with exceptionally powerful wettability switch capabilities and liquid-repellent properties through an extremely simple one-step electrochemical deposition process. The wettability switch and manipulative liquid-repellent properties are enabled by orientation change of the dodecyl sulfate ions ionically bonded to the porous membranes during electrodeposition. The porous membrane with adjustable wettability enables it to trap different lubricants on demand within the pores to form liquid-infused porous surfaces with varied liquid-repellent properties. We have demonstrated the application of the (liquid-infused) porous membrane in encryption, controllable droplet transfer, and water harvesting. Moreover, the silver porous membrane can be coated onto a copper mesh, forming a smart antifouling liquid gate capable of allowing water or oil to pass through on request.

| S-EPMC6824854 | biostudies-literature

Rational disruption of the oligomerization of the mini-ferritin E. coli DPS through protein-protein interface mutation.

Project description:DNA-binding protein from starved cells (DPS), a mini-ferritin capable of self-assembling into a 12-meric nano-cage, was chosen as the basis for an alanine-shaving mutagenesis study to investigate the importance of key amino acid residues, located at symmetry-related protein-protein interfaces, in controlling protein stability and self-assembly. Nine mutants were designed through simple inspection, synthesized, and subjected to transmission electron microscopy, circular dichroism, size exclusion chromatography, and "virtual alanine scanning" computational analysis. The data indicate that many of these residues may be hot spot residues. Most remarkably, two residues, R83 and R133, were observed to shift the oligomerization state to ~50% dimer. Based on the hypothesis that these two residues constitute a "hot strip," located at the ferritin-like threefold axis, the double mutant was generated which completely shuts down detectable formation of 12-mer in solution, favoring a cooperatively folded dimer. The fact that this effect logically builds upon the single mutants emphasizes that complex self-assembly has the potential to be manipulated rationally. This study should have an impact on the fundamental understanding of the assembly of DPS protein cages specifically and protein quaternary structure in general. In addition, as there is much interest in applying these and similar systems to the templation of nano-materials and drug delivery, the ability to control this ferritin's oligomerization state and stability could prove especially valuable.

| S-EPMC3267954 | biostudies-literature

Structural basis of the zinc- and terbium-mediated inhibition of ferroxidase activity in Dps ferritin-like proteins.

Project description:Streptococcus suis Dpr is an iron-binding protein involved in oxidative stress resistance. It belongs to the bacterial Dps protein family whose members form dodecameric assemblies. Previous studies have shown that zinc and terbium inhibit iron incorporation in Listeria innocua Dps protein. In order to gain structural insights into the inhibitory effect of zinc and terbium, the crystal structures of Streptococcus suis Dpr complexes with these ions were determined at 1.8 A and 2.1 A, respectively. Both ions were found to bind at the ferroxidase center and in the same location as iron. In addition, a novel zinc-binding site formed by His40 and His44 was identified. Both His residues were found to be present within all known Streptococcus suis Dpr variants and in Streptococcus pneumoniae, Streptococcus gordonii, and Streptococcus sanguinis Dpr proteins. Amino acid sequence alignment of Dpr with other Dps family members revealed that His44 is highly conserved, in contrast to His40. The inhibitory effect of zinc and terbium on iron oxidation in Dpr was studied in vitro, and it was found that both ions at concentrations >0.2 mM almost completely abolish iron binding. These results provide a structural basis for the inhibitory effect of zinc and terbium in the Dps family of proteins, and suggest a potential role of the Dps proteins in zinc detoxification mechanisms involving the second zinc-binding site.

| S-EPMC2525527 | biostudies-literature

Interfacial metal and antibody recognition.

Project description:The unique ligation properties of metal ions are widely exploited by proteins, with approximately one-third of all proteins estimated to be metalloproteins. Although antibodies use various mechanisms for recognition, to our knowledge, none has ever been characterized that uses an interfacial metal. We previously described a family of CD4-reactive antibodies, the archetype being Q425. CD4:Q425 engagement does not interfere with CD4:HIV-1 gp120 envelope glycoprotein binding, but it blocks subsequent steps required for viral entry. Here, we use surface-plasmon resonance to show that Q425 requires calcium for recognition of CD4. Specifically, Q425 binding of calcium resulted in a 55,000-fold enhancement in affinity for CD4. X-ray crystallographic analyses of Q425 in the presence of Ca(2+), Ba(2+), or EDTA revealed an exposed metal-binding site, partially coordinated by five atoms contributed from four antibody complementarity-determining regions. The results suggest that Q425 recognition of CD4 involves direct ligation of antigen by the Q425-held calcium, with calcium binding each ligating atom of CD4 with approximately 1.5 kcal/mol of binding energy. This energetic contribution, which is greater than that from a typical protein atom, demonstrates how interfacial metal ligation can play a unique role in antigen recognition.

| S-EPMC1237054 | biostudies-literature

Seawater biofilm on plastic and metal surfaces

Project description:Bacterial cell numbers and community structures of seawater biofilm differed depending on the attachment substratum

| PRJEB20120 | ENA

Role of the dispersion force in modeling the interfacial properties of molecule-metal interfaces: adsorption of thiophene on copper surfaces.

Project description:We present density functional theory calculations of the geometry, adsorption energy and electronic structure of thiophene adsorbed on Cu(111), Cu(110) and Cu(100) surfaces. Our calculations employ dispersion corrections and self-consistent van der Waals density functionals (vdW-DFs). In terms of speed and accuracy, we find that the dispersion-energy-corrected Revised Perdue-Burke-Enzerhof (RPBE) functional is the "best balanced" method for predicting structural and energetic properties, while vdW-DF is also highly accurate if a proper exchange functional is used. Discrepancies between theory and experiment in molecular geometry can be solved by considering x-ray generated core-holes. However, the discrepancy concerning the adsorption site for thiophene/Cu(100) remains unresolved and requires both further experiments and deeper theoretical analysis. For all the interfaces, the PBE functional reveals a covalent bonding picture which the inclusion of dispersive contributions does not change to a vdW one. Our results provide a comprehensive understanding of the role of dispersive forces in modelling molecule-metal interfaces.

| S-EPMC4030267 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data