Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Electrostatic regulation of blue copper sites.

ABSTRACT: In the last 50 years, the blue copper proteins became central targets of investigation. Extensive experiments focused on the Cu coordination to probe the effect of local perturbations on its properties. We found that local electric fields, generated by charged residues evolutionarily placed throughout the protein edifice, mainly second sphere, but also more remotely, constitute an additional significant factor regulating blue copper proteins. These fields are not random, but exhibit a highly specific directionality, negative with respect to the and vectors in the Cu first shell. The field magnitude contributes to fine-tuning of the geometric and electronic properties of Cu sites in individual blue copper proteins. Specifically, the local electric fields evidently control the Cu-S_Met bond distance, Cu(ii)-S_Cys bond covalency, and the energies of the frontier molecular orbitals, which, in turn, govern the Cu(ii/i) reduction potential and the relative absorption intensities at 450 nm and 600 nm.

SUBMITTER: Bim D

PROVIDER: S-EPMC8447924 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Electrostatic regulation of blue copper sites.

Bím Daniel D Alexandrova Anastassia N AN

Chemical science 20210727 34

In the last 50 years, the blue copper proteins became central targets of investigation. Extensive experiments focused on the Cu coordination to probe the effect of local perturbations on its properties. We found that local electric fields, generated by charged residues evolutionarily placed throughout the protein edifice, mainly second sphere, but also more remotely, constitute an additional significant factor regulating blue copper proteins. These fields are not random, but exhibit a highly spe ...[more]

PMID: 34667549

Similar Datasets

Electrostatic steering at acetylcholine binding sites.

Project description:The electrostatic environments near the acetylcholine binding sites on the nicotinic acetylcholine receptor (nAChR) and acetylcholinesterase were measured by diffusion-enhanced fluorescence energy transfer (DEFET) to determine the influence of long-range electrostatic interactions on ligand binding kinetics and net binding energy. Changes in DEFET from variously charged Tb3+ -chelates revealed net potentials of -20 mV at the nAChR agonist sites and -14 mV at the entrance to the AChE active site, in physiological ionic strength conditions. The potential at the alphadelta-binding site of the nAChR was determined independently in the presence of d-tubocurarine to be -14 mV; the calculated potential at the alphagamma-site was approximately threefold stronger than at the alphadelta-site. By determining the local potential in increasing ionic strength, Debye-Hückel theory predicted that the potentials near the nAChR agonist binding sites are constituted by one to three charges in close proximity to the binding site. Examination of the binding kinetics of the fluorescent acetylcholine analog dansyl-C6-choline at ionic strengths from 12.5 to 400 mM revealed a twofold decrease in association rate. Debye-Hückel analysis of the kinetics revealed a similar charge distribution as seen by changes in the potentials. To determine whether the experimentally determined potentials are reflected by continuum electrostatics calculations, solutions to the nonlinear Poisson-Boltzmann equation were used to compute the potentials expected from DEFET measurements from high-resolution models of the nAChR and AChE. These calculations are in good agreement with the DEFET measurements for AChE and for the alphagamma-site of the nAChR. We conclude that long-range electrostatic interactions contribute -0.3 and -1 kcal/mol to the binding energy at the nAChR alphadelta- and alphagamma-sites due to an increase in association rates.

| S-EPMC1518644 | biostudies-literature

Thermodynamic equilibrium between blue and green copper sites and the role of the protein in controlling function.

Project description:A combination of spectroscopies and density functional theory calculations indicate that there are large temperature-dependent absorption spectral changes present in green nitrite reductases (NiRs) due to a thermodynamic equilibrium between a green and a blue type 1 (T1) copper site. The axial methionine (Met) ligand is unconstrained in the oxidized NiRs, which results in an enthalpically favored (DeltaH approximately 4.6 kcal/mol) Met-bound green copper site at low temperatures, and an entropically favored (TDeltaS approximately 4.5 kcal/mol, at room temperature) Met-elongated blue copper site at elevated temperatures. In contrast to the NiRs, the classic blue copper sites in plastocyanin and azurin show no temperature-dependent behavior, indicating that a single species is present at all temperatures. For these blue copper proteins, the polypeptide matrix opposes the gain in entropy that would be associated with the loss of the weak axial Met ligand at physiological temperatures by constraining its coordination to copper. The potential energy surfaces of Met binding indicate that it stabilizes the oxidized state more than the reduced state. This provides a mechanism to tune down the reduction potential of blue copper sites by >200 mV.

| S-EPMC2664060 | biostudies-literature

Copper active sites in biology.

Project description: Not available

| S-EPMC4040215 | biostudies-literature

Cu(I) analysis of blue copper proteins.

Project description:A simple colorimetric test for the Cu(I) content in blue copper proteins is described. The procedure is based on the formation of a complex between Cu(I) and 2,2'-biquinoline in an acetic acid medium. Analyses of spinach plastocyanin, Pseudomonas aeruginosa azurin and Rhus vernicifera stellacyanin show that the cysteine residue in the type 1 site does not induce Cu(II) reduction under our conditions. There is evidence in laccase samples for the presence of an endogenous reductant that can reduce 0.14 +/- 0.04 mol of Cu(II)/mol of protein; however, the addition of EDTA eliminates the interference. The analysis shows that 25 +/- 2% of the type 3 copper ions are in the reduced form in the resting enzyme and that 80 +/- 15% of the type 3 copper ions are reduced in preparations of type-2-depleted laccase. There is growing interest in the development of chemically modified forms of laccase, and our method should be very useful for establishing the valence state of the metal centres in the various derivatives.

| S-EPMC1135515 | biostudies-other

Prediction of protein-protein interaction sites using electrostatic desolvation profiles.

Project description:Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces.

| S-EPMC2862153 | biostudies-literature

Phylogenetic analysis of six-domain multi-copper blue proteins.

Project description:Multicopper blue proteins, composed of several repetitive copper-binding domains similar to one-domain cupredoxin-like proteins, were found in almost all organisms. They are classified into the three different groups, based on their two-, three- or six-domain organization. We found orthologs of chordate six-domain copper-binding proteins in animals, plants, bacteria and archea. The phylogenetic analysis of 183 multicopper blue proteins and their copper-binding sites comparison make us think that all the modern six-domain blue proteins have originated from the common ancestral six-domain protein in the process of gene duplication and copper-binding sites loss as a result of amino acid substitutions.

| S-EPMC3600357 | biostudies-literature

Using internal electrostatic fields to manipulate the valence manifolds of copper complexes.

Project description:A series of tetradentate tris(phosphinimine) ligands (R3P3tren) was developed and bound to CuI to form the trigonal pyramidal, C 3v-symmetric cuprous complexes [R3P3tren-Cu][BArF 4] (1PR3) (PR3 = PMe3, PMe2Ph, PMePh2, PPh3, PMe2(NEt2), BArF 4 = B(C6F5)4). Electrochemical studies on the CuI complexes were undertaken, and the permethylated analog, 1PMe3, was found to display an unprecedentedly cathodic CuI/CuII redox potential (-780 mV vs. Fc/Fc+ in isobutyronitrile). Elucidation of the electronic structures of 1PR3 via density functional theory (DFT) studies revealed atypical valence manifold configurations, resulting from strongly σ-donating phosphinimine moieties in the xy-plane that destabilize 2e (d xy /d x 2-y 2 ) orbital sets and uniquely stabilized a 1 (d z 2 ) orbitals. Support is provided that the a 1 stabilizations result from intramolecular electrostatic fields (ESFs) generated from cationic character on the phosphinimine moieties in R3P3tren. This view is corroborated via 1-dimensional electrostatic potential maps along the z-axes of 1PR3 and their isostructural analogues. Experimental validation of this computational model is provided upon oxidation of 1PMe3 to the cupric complex [Me3P3tren-Cu][OTf]2 (2PMe3), which displays a characteristic Jahn-Teller distortion in the form of a see-saw, pseudo-C s-symmetric geometry. A systematic anodic shift in the potential of the CuI/CuII redox couple as the steric bulk in the secondary coordination sphere increases is explained through the complexes' diminishing ability to access the ideal C s-symmetric geometry upon oxidation. The observations and calculations discussed in this work support the presence of internal electrostatic fields within the copper complexes, which subsequently influence the complexes' properties via a method orthogonal to classic ligand field tuning.

| S-EPMC8179517 | biostudies-literature

Inner- and outer-sphere metal coordination in blue copper proteins.

Project description:Blue copper proteins (BCPs) comprise classic cases of Nature's profound control over the electronic structures and chemical reactivity of transition metal ions. Early studies of BCPs focused on their inner coordination spheres, that is, residues that directly coordinate Cu. Equally important are the electronic and geometric perturbations to these ligands provided by the outer coordination sphere. In this tribute to Hans Freeman, we review investigations that have advanced the understanding of how inner-sphere and outer-sphere coordination affects biological Cu properties.

| S-EPMC3434318 | biostudies-literature

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.

Project description:A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding sites were initially analysed for accessibility, electrostatic potential, residue propensity, hydrophobicity and residue conservation. From this, it was observed that the DNA-binding sites were, in general, amongst the top 10% of patches with the largest positive electrostatic scores. This knowledge led to the development of a prediction method in which patches of surface residues were selected such that they excluded residues with negative electrostatic scores. This method was used to make predictions for a data set of 56 non-homologous DNA-binding proteins. Correct predictions made for 68% of the data set.

| S-EPMC291864 | biostudies-literature

Experimental electronic structures of copper complexes with a biphenyldiimino dithioether - a model for blue copper proteins.

Project description:The experimental electron density distributions in two coordination compounds - one with a central Cu(I) atom and the other with Cu(II), coordinated by the same biphenyldiimino dithioether (bite) type of ligand - have been obtained from high-resolution X-ray reflection data to model the possible electron predisposition for the redox reaction in blue copper proteins. The bite ligand has been adapted to the conformation required by the central atom.

| S-EPMC11878452 | biostudies-literature

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