Theoretical Studies of Metal Ion Selectivity.†2. DFT Calculations of Complexation Energies of Selected Transition Metal Ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in Metal-Binding Sites of Metalloproteins

2002 ◽  
Vol 106 (15) ◽  
pp. 3855-3866 ◽  
Author(s):  
Lubomír Rulíšek ◽  
Zdeněk Havlas
Keyword(s):  
Transition Metal ◽  
Dft Calculations ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Ion Selectivity ◽  
Transition Metal Ions ◽  
Theoretical Studies ◽  
Metal Binding Sites ◽  
Metal Ion Selectivity

scholarly journals Exploring the structure and function of Thermotoga maritima CorA reveals the mechanism of gating and ion selectivity in Co2+/Mg2+ transport

2013 ◽  
Vol 451 (3) ◽  
pp. 365-374 ◽  
Author(s):  
Nurhuda Nordin ◽  
Albert Guskov ◽  
Terri Phua ◽  
Newsha Sahaf ◽  
Yu Xia ◽  
...  
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Thermotoga Maritima ◽  
Ion Selectivity ◽  
Metal Binding Sites ◽  
Gating Mechanism ◽  
Structural Details ◽  
And Function ◽  
Conserved Amino Acids

The CorA family of divalent cation transporters utilizes Mg2+ and Co2+ as primary substrates. The molecular mechanism of its function, including ion selectivity and gating, has not been fully characterized. Recently we reported a new structure of a CorA homologue from Methanocaldococcus jannaschii, which provided novel structural details that offered the conception of a unique gating mechanism involving conversion of an open hydrophilic gate into a closed hydrophobic one. In the present study we report functional evidence for this novel gating mechanism in the Thermotoga maritima CorA together with an improved crystal structure of this CorA to 2.7 Å (1 Å=0.1 nm) resolution. The latter reveals the organization of the selectivity filter to be similar to that of M. jannaschii CorA and also the previously unknown organization of the second signature motif of the CorA family. The proposed gating is achieved by a helical rotation upon the binding of a metal ion substrate to the regulatory binding sites. Additionally, our data suggest that the preference of this CorA for Co2+ over Mg2+ is controlled by the presence of threonine side chains in the channel. Finally, the roles of the intracellular metal-binding sites have been assigned to increased thermostability and regulation of the gating. These mechanisms most likely apply to the entire CorA family as they are regulated by the highly conserved amino acids.

scholarly journals Metal-binding sites of concanavalin A and their role in the binding of α-methyl d-glucopyranoside

1968 ◽  
Vol 109 (4) ◽  
pp. 669-672 ◽  
Author(s):  
A. Joseph Kalb ◽  
Alexander Levitzki
Keyword(s):  
Transition Metal ◽  
Concanavalin A ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Ion Binding ◽  
Transition Metal Ion ◽  
Metal Binding Sites ◽  
Ion Binding Sites

Binding of a transition metal ion to specific sites in concanavalin A induces the formation of specific Ca2+ ion-binding sites. Sites for binding α-methyl d-glucopyranoside exist only when a transition metal ion and Ca2+ ion are bound.

scholarly journals Transition metal ion FRET to measure short-range distances at the intracellular surface of the plasma membrane

2016 ◽  
Vol 147 (2) ◽  
pp. 189-200 ◽  
Author(s):  
Sharona E. Gordon ◽  
Eric N. Senning ◽  
Teresa K. Aman ◽  
William N. Zagotta
Keyword(s):  
Plasma Membrane ◽  
Transition Metal ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Head Group ◽  
Transition Metal Ion ◽  
Metal Binding Sites

Biological membranes are complex assemblies of lipids and proteins that serve as platforms for cell signaling. We have developed a novel method for measuring the structure and dynamics of the membrane based on fluorescence resonance energy transfer (FRET). The method marries four technologies: (1) unroofing cells to isolate and access the cytoplasmic leaflet of the plasma membrane; (2) patch-clamp fluorometry (PCF) to measure currents and fluorescence simultaneously from a membrane patch; (3) a synthetic lipid with a metal-chelating head group to decorate the membrane with metal-binding sites; and (4) transition metal ion FRET (tmFRET) to measure short distances between a fluorescent probe and a transition metal ion on the membrane. We applied this method to measure the density and affinity of native and introduced metal-binding sites in the membrane. These experiments pave the way for measuring structural rearrangements of membrane proteins relative to the membrane.

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.

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.

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