scholarly journals Unravelling the Structure of the Tetrahedral Metal-Binding Site in METP3 through an Experimental and Computational Approach

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5221
Author(s):  
Salvatore La Gatta ◽  
Linda Leone ◽  
Ornella Maglio ◽  
Maria De Fenza ◽  
Flavia Nastri ◽  
...  
Keyword(s):  
Metal Ions ◽  
Binding Site ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Structural Determinants ◽  
Binding Properties ◽  
Tetrahedral Geometry ◽  
Design Synthesis ◽  
Metal Binding Sites

Understanding the structural determinants for metal ion coordination in metalloproteins is a fundamental issue for designing metal binding sites with predetermined geometry and activity. In order to achieve this, we report in this paper the design, synthesis and metal binding properties of METP3, a homodimer made up of a small peptide, which self assembles in the presence of tetrahedrally coordinating metal ions. METP3 was obtained through a redesign approach, starting from the previously developed METP molecule. The undecapeptide sequence of METP, which dimerizes to house a Cys4 tetrahedral binding site, was redesigned in order to accommodate a Cys2His2 site. The binding properties of METP3 were determined toward different metal ions. Successful assembly of METP3 with Co(II), Zn(II) and Cd(II), in the expected 2:1 stoichiometry and tetrahedral geometry was proven by UV-visible spectroscopy. CD measurements on both the free and metal-bound forms revealed that the metal coordination drives the peptide chain to fold into a turned conformation. Finally, NMR data of the Zn(II)-METP3 complex, together with a retrostructural analysis of the Cys-X-X-His motif in metalloproteins, allowed us to define the model structure. All the results establish the suitability of the short METP sequence for accommodating tetrahedral metal binding sites, regardless of the first coordination ligands.

scholarly journals Investigation of the nature of the two metal-binding sites in 5-aminolaevulinic acid dehydratase from Escherichia coli

1994 ◽  
Vol 300 (2) ◽  
pp. 373-381 ◽  
Author(s):  
P Spencer ◽  
P M Jordan
Keyword(s):  
Escherichia Coli ◽  
Metal Ions ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Protein Fluorescence ◽  
Metal Binding Sites ◽  
Aminolaevulinic Acid ◽  
Acid Dehydratase ◽  
Aminolaevulinic Acid Dehydratase

Two distinct metal-binding sites, termed alpha and beta, have been characterized in 5-aminolaevulinic acid dehydratase from Escherichia coli. The alpha-site binds a Zn2+ ion that is essential for catalytic activity. This site can also utilize other metal ions able to function as a Lewis acid in the reaction mechanism, such as Mg2+ or Co2+. The beta-site is exclusively a transition-metal-ion-binding site thought to be involved in protein conformation, although a metal bound at this site only appears to be essential for activity if Mg2+ is to be bound at the alpha-site. The alpha- and beta-sites may be distinguished from one another by their different abilities to bind divalent-metal ions at different pH values. The occupancy of the beta-site with Zn2+ results in a decrease of protein fluorescence at pH 6. Occupancy of the alpha- and beta-sites with Co2+ results in u.v.-visible spectral changes. Spectroscopic studies with Co2+ have tentatively identified three cysteine residues at the beta-site and one at the alpha-site. Reaction with N-ethyl[14C]maleimide preferentially labels cysteine-130 at the alpha-site when Co2+ occupies the beta-site.

scholarly journals Computational approaches for de novo design and redesign of metal-binding sites on proteins

2017 ◽  
Vol 37 (2) ◽  
Author(s):  
Gunseli Bayram Akcapinar ◽  
Osman Ugur Sezerman
Keyword(s):  
Metal Ions ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
De Novo ◽  
De Novo Design ◽  
Ion Binding ◽  
Chemical Transformations ◽  
Metal Ion Binding ◽  
Metal Binding Sites

Metal ions play pivotal roles in protein structure, function and stability. The functional and structural diversity of proteins in nature expanded with the incorporation of metal ions or clusters in proteins. Approximately one-third of these proteins in the databases contain metal ions. Many biological and chemical processes in nature involve metal ion-binding proteins, aka metalloproteins. Many cellular reactions that underpin life require metalloproteins. Most of the remarkable, complex chemical transformations are catalysed by metalloenzymes. Realization of the importance of metal-binding sites in a variety of cellular events led to the advancement of various computational methods for their prediction and characterization. Furthermore, as structural and functional knowledgebase about metalloproteins is expanding with advances in computational and experimental fields, the focus of the research is now shifting towards de novo design and redesign of metalloproteins to extend nature’s own diversity beyond its limits. In this review, we will focus on the computational toolbox for prediction of metal ion-binding sites, de novo metalloprotein design and redesign. We will also give examples of tailor-made artificial metalloproteins designed with the computational toolbox.

Metal Ion Binding Properties of Perfluorosulfonate Membranes by Laser Excitation Spectroscopy

1988 ◽  
Vol 42 (2) ◽  
pp. 293-295 ◽  
Author(s):  
E. K. L. Wong ◽  
G. L. Richmond
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Laser Excitation ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Binding Properties ◽  
Metal Binding Sites ◽  
Fluorescence Measurements ◽  
Experimental Parameters

The metal ion binding properties of the perfluorosulfonate membrane Nafion® have been investigated in this study. The experiments involve laser-induced fluorescence measurements of europium (III) ions which are bound to the membrane. By the exploitation of the hypersensitivity of the D → F transitions of europium (III) to the ligand binding environment, the properties of the metal binding sites have been analyzed as a function of various experimental parameters. The spectra and fluorescence lifetime measurements provide evidence for distinct metal binding sites within the polymer, each of which is sensitive to the conditions of the membrane preparation.

scholarly journals Binding of Gd3+to the neuronal signalling protein calexcitin identifies an exchangeable Ca2+-binding site

2016 ◽  
Vol 72 (4) ◽  
pp. 276-281
Author(s):  
Lucas Chataigner ◽  
Jingxu Guo ◽  
Peter T. Erskine ◽  
Alun R. Coker ◽  
Steve P. Wood ◽  
...  
Keyword(s):  
Metal Ions ◽  
Binding Site ◽  
Metal Binding ◽  
Calcium Signalling ◽  
Specific Protein ◽  
Metal Binding Sites ◽  
Calcium Sensing ◽  
Neuronal Signalling ◽  
Ef Hand ◽  
Ef Hands

Calexcitin was first identified in the marine snailHermissenda crassicornisas a neuronal-specific protein that becomes upregulated and phosphorylated in associative learning. Calexcitin possesses four EF-hand motifs, but only the first three (EF-1 to EF-3) are involved in binding metal ions. Past work has indicated that under physiological conditions EF-1 and EF-2 bind Mg2+and Ca2+, while EF-3 is likely to bind only Ca2+. The fourth EF-hand is nonfunctional owing to a lack of key metal-binding residues. The aim of this study was to use a crystallographic approach to determine which of the three metal-binding sites of calexcitin is most readily replaced by exogenous metal ions, potentially shedding light on which of the EF-hands play a `sensory' role in neuronal calcium signalling. By co-crystallizing recombinant calexcitin with equimolar Gd3+in the presence of trace Ca2+, EF-1 was shown to become fully occupied by Gd3+ions, while the other two sites remain fully occupied by Ca2+. The structure of the Gd3+–calexcitin complex has been refined to anRfactor of 21.5% and anRfreeof 30.4% at 2.2 Å resolution. These findings suggest that EF-1 of calexcitin is the Ca2+-binding site with the lowest selectivity for Ca2+, and the implications of this finding for calcium sensing in neuronal signalling pathways are discussed.

Characterisation of Metal Binding Sites for 8-Azaguanine and 8-Azahypoxanthine Derivatives Synthesis and X-Ray Structural Analysis of Methylmercury(II) and Zinc(II) Complexes

1986 ◽  
Vol 41 (9) ◽  
pp. 1117-1122 ◽  
Author(s):  
W. S. Sheldrick ◽  
P. Bell
Keyword(s):  
Structural Analysis ◽  
Binding Site ◽  
Metal Binding ◽  
Binding Sites ◽  
Antineoplastic Agent ◽  
X Ray ◽  
Metal Binding Sites ◽  
Ph Values ◽  
Ph Range

Abstract The complexes [(CH3Hg)AGuaH ] (1) and [(CH3Hg)2AGua] • H2O (2) have been isolated from aqueous 1:1 and 2:1 solutions of CH3HgOH and 8 -azaguanine (AGuaH2) at respective pH values of 5 and 9. Only one CH3Hg+ complex of 8 -azahypoxanthine (AHxH2), namely [(CH3Hg)2AHx] (3), could be isolated under analogous conditions. X-ray structural analyses established N1 and N9 as metal binding sites in 3 and N9 as the coordination position in [Zn(H2O)4(AHxH)2] (4). With 8-aza-9-benzylhypoxanthine (9-BzAHxH) only one CH3Hg+ complex [(CH3Hg)9-BzAHx] (5) could be isolated in the pH range 2-10. N1 was established by X-ray structural analysis as the binding site. The relevance o f these findings to an understanding of ligand behaviour of the antineoplastic agent 8 -azaguanine is discussed.

scholarly journals Specificity and affinity of binding of phosphate-containing compounds to CheY protein

1992 ◽  
Vol 287 (2) ◽  
pp. 533-543 ◽  
Author(s):  
L Kar ◽  
P Z De Croos ◽  
S J Roman ◽  
P Matsumura ◽  
M E Johnson
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Bacterial Chemotaxis ◽  
Phosphate Binding ◽  
Metal Binding Sites ◽  
Low Concentrations ◽  
Bivalent Metal Ions ◽  
Proton Resonances ◽  
Inorganic Phosphates

1H- and 31P-n.m.r. have been used to study the interaction of the bacterial chemotaxis protein, CheY, with ATP and a variety of other phosphates in the presence and absence of bivalent metal ions. In the metal-bound conformation, CheY will bind nucleotide phosphates and phosphates in general, while in the metal-free conformation CheY loses its affinity for phosphates. In the presence of low concentrations of nitroxide-spin-labelled ATP (SL-ATP), specific proton resonances of metal-bound CheY are suppressed, indicating that ATP binds to a specific site on this metal-bound form of the protein. These studies also show that the same resonances are affected by the binding of SL-ATP and Mn2+, indicating that the phosphate- and metal-binding sites are close to each other and to Asp-57 (the site of phosphorylation in CheY). 1H- and 31P-n.m.r. studies using ATP, GTP, TTP, UTP, ADP, AMP and inorganic phosphates show that the binding is not specific for adenine, and does not involve the base directly, but is mediated primarily by the phosphate groups. Experiments with a phosphorylation mutant (Asp-13-->Asn) suggest that the observed phosphate binding and activation of CheY by phosphorylation may be related. Our results indicate that the conformational change and charge interactions brought about by the binding of a metal ion at the active site are required for CheY to interact with a phosphate. These studies also demonstrate the utility of spin-label-induced relaxation in conjunction with two-dimensional-n.m.r. measurements for exploring ligand-binding sites.

Probing Metal Ion Complexation of Ligands with Multiple Metal Binding Sites: The Case of Spiropyrans

2016 ◽  
Vol 22 (39) ◽  
pp. 13976-13984 ◽  
Author(s):  
Michele Baldrighi ◽  
Giulia Locatelli ◽  
John Desper ◽  
Christer B. Aakeröy ◽  
Silvia Giordani
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Metal Ion Complexation ◽  
Metal Binding Sites ◽  
Ion Complexation

Multicomponent Kinetic Analysis of Trace Metal Binding Sites on Iron Hydrous Oxide Colloids

1988 ◽  
Vol 23 (3) ◽  
pp. 379-387 ◽  
Author(s):  
Donald W. Gutzman ◽  
Cooper H. Langford
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Base Hydrolysis ◽  
Diffusion Control ◽  
Hydrous Oxide ◽  
Ion Release ◽  
Metal Binding Sites ◽  
Metal Ion Release ◽  
Colloidal Species

Abstract The adsorption of copper(II) on a hydrous oxide colloid of iron formed by base hydrolysis in the presence of the adsorbate metal has been studied in two ways. Filtration-AAS of equilibrated solutions yielded data which fit well to a single variant adsorption isotherm even at high adsorbate metal concentration thus precluding the need for multivariant fitting. These same colloidal species were kinetically analyzed by reaction of copper with the chromophore reagent EHTTT (a = 13700 Mࢤ1 cmࢤ1 at 434 nm) which revealed the presence of three components, other than the very labile “free” species. Kinetic differentiation of thermodynamically similar sites may result from diffusion control of metal ion release.

Sign in / Sign up

Export Citation Format

Share Document