Optimizing the Metal Binding Parameters of an EF-Hand-Like Calcium Chelation Loop:  Coordinating Side Chains Play a More Important Tuning Role than Chelation Loop Flexibility†

Biochemistry ◽  
1997 ◽  
Vol 36 (32) ◽  
pp. 9917-9926 ◽  
Author(s):  
Steven K. Drake ◽  
Michael A. Zimmer ◽  
Cory L. Miller ◽  
Joseph J. Falke
Keyword(s):  
Metal Binding ◽  
Side Chains ◽  
Binding Parameters ◽  
Calcium Chelation ◽  
Ef Hand ◽  
Loop Flexibility

scholarly journals Molecular Tuning of an EF-Hand-like Calcium Binding Loop

1997 ◽  
Vol 110 (2) ◽  
pp. 173-184 ◽  
Author(s):  
Steven K. Drake ◽  
Michael A. Zimmer ◽  
Craig Kundrot ◽  
Joseph J. Falke
Keyword(s):  
Calcium Binding ◽  
Ion Selectivity ◽  
Side Chain ◽  
Binding Motif ◽  
Side Chains ◽  
Binding Parameters ◽  
Size Selectivity ◽  
The Third ◽  
Ef Hand ◽  
Binding Loop

Calcium binding and signaling orchestrate a wide variety of essential cellular functions, many of which employ the EF-hand Ca2+ binding motif. The ion binding parameters of this motif are controlled, in part, by the structure of its Ca2+ binding loop, termed the EF-loop. The EF-loops of different proteins are carefully specialized, or fine-tuned, to yield optimized Ca2+ binding parameters for their unique cellular roles. The present study uses a structurally homologous Ca2+ binding loop, that of the Escherichia coli galactose binding protein, as a model for the EF-loop in studies examining the contribution of the third loop position to intramolecular tuning. 10 different side chains are compared at the third position of the model EF-loop with respect to their effects on protein stability, sugar binding, and metal binding equilibria and kinetics. Substitution of an acidic Asp side chain for the native Asn is found to generate a 6,000-fold increase in the ion selectivity for trivalent over divalent cations, providing strong support for the electrostatic repulsion model of divalent cation charge selectivity. Replacement of Asn by neutral side chains differing in size and shape each alter the ionic size selectivity in a similar manner, supporting a model in which large-ion size selectivity is controlled by complex interactions between multiple side chains rather than by the dimensions of a single coordinating side chain. Finally, the pattern of perturbations generated by side chain substitutions helps to explain the prevalence of Asn and Asp at the third position of natural EF-loops and provides further evidence supporting the unique kinetic tuning role of the gateway side chain at the ninth EF-loop position.

scholarly journals Synthesis of New Derivatives of BEDT-TTF: Installation of Alkyl, Ethynyl, and Metal-Binding Side Chains and Formation of Tris(BEDT-TTF) Systems

2021 ◽  
Vol 7 (8) ◽  
pp. 110
Author(s):  
Songjie Yang ◽  
Matteo Zecchini ◽  
Andrew Brooks ◽  
Sara Krivickas ◽  
Desiree Dalligos ◽  
...  
Keyword(s):  
Metal Binding ◽  
Tricarboxylic Acid ◽  
Metal Salts ◽  
Side Chain ◽  
Side Chains ◽  
Ethynyl Group ◽  
X Ray ◽  
Transition Metal Salts ◽  
Alkyl Side Chains ◽  
Derivatives Of

The syntheses of new BEDT-TTF derivatives are described. These comprise BEDT-TTF with one ethynyl group (HC≡C-), with two (n-heptyl) or four (n-butyl) alkyl side chains, with two trans acetal (-CH(OMe)2) groups, with two trans aminomethyl (-CH2NH2) groups, and with an iminodiacetate (-CH2N(CH2CO2−)2 side chain. Three transition metal salts have been prepared from the latter donor, and their magnetic properties are reported. Three tris-donor systems are reported bearing three BEDT-TTF derivatives with ester links to a core derived from benzene-1,3,5-tricarboxylic acid. The stereochemistry and molecular structure of the donors are discussed. X-ray crystal structures of two BEDT-TTF donors are reported: one with two CH(OMe)2 groups and with one a -CH2N(CH2CO2Me)2 side chain.

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.

The effect of non-coordinating side chains on the metal binding affinities of peptides of histidine

Polyhedron ◽  
2013 ◽  
Vol 62 ◽  
pp. 7-17 ◽  
Author(s):  
Ildikó Turi ◽  
Daniele Sanna ◽  
Eugenio Garribba ◽  
Giuseppe Pappalardo ◽  
Imre Sóvágó
Keyword(s):  
Metal Binding ◽  
Side Chains ◽  
Binding Affinities

Enhancement of enzymatic activity for myoglobins by modification of heme-propionate side chains

2004 ◽  
Vol 08 (03) ◽  
pp. 255-264 ◽  
Author(s):  
Takashi Hayashi ◽  
Hideaki Sato ◽  
Takashi Matsuo ◽  
Takaaki Matsuda ◽  
Yutaka Hitomi ◽  
...  
Keyword(s):  
Binding Site ◽  
Metal Binding ◽  
Protein Function ◽  
Site Directed Mutagenesis ◽  
Side Chain ◽  
Side Chains ◽  
Cytochrome P450 Enzyme ◽  
Prosthetic Group ◽  
Heme Pocket ◽  
P450 Enzyme

The modification of myoglobin is an attractive process not only for understanding its molecular mechanism but also for engineering the protein function. The strategy of myoglobin functionalization can be divided into at least two approaches: site-directed mutagenesis and reconstitution with a non-natural prosthetic group. The former method enables us to mainly modulate the physiological function, while the latter has the advantage of introducing a new function on the protein. Particularly, replacement of the native hemin with an artificially created hemin having hydrophobic moieties at the terminal of the heme-propionate side chains serves as an appropriate substrate-binding site near the heme pocket, and consequently enhances the peroxidase and peroxygenase activities for the reconstituted myoglobin. In addition, the incorporation of the synthetic hemin bearing modified heme-propionates into an appropriate apomyoglobin mutant drastically enhances the peroxidase activity. In contrast, to convert myoglobin into a cytochrome P450 enzyme, a flavin moiety as an electron transfer mediator was introduced at the terminal of the heme-propionate side chain. The flavomyoglobin catalyzes the deformylation of 2-phenylpropanal in the presence of NADH under aerobic conditions through the peroxoanion formation from the oxygenated species. In addition, modification of the heme-propionate side chains has an significant influence on regulating the reactivity of the horseradish peroxidase. Furthermore, the heme-propionate side chain can form a metal binding site with a carboxylate residue in the heme pocket. These studies indicate that modification of the heme-propionate side chains can be a new and effective way to engineer functions for the hemoproteins.

scholarly journals A comparative CD and fluorescence study of a series of model calcium-binding peptides.

1999 ◽  
Vol 46 (3) ◽  
pp. 673-677 ◽  
Author(s):  
G Goch ◽  
H Kozłowska ◽  
A Wójtowicz ◽  
A Bierzyński
Keyword(s):  
Metal Binding ◽  
Calcium Binding ◽  
Helical Structure ◽  
Homoserine Lactone ◽  
Lanthanide Ions ◽  
C Terminus ◽  
Helical Segment ◽  
Ef Hand ◽  
N Terminus ◽  
Negative Effect

Lanthanide-saturated peptides analogous to calcium-binding loops of EF-hand proteins can be used to stabilize the alpha-helical structure of peptide or protein segments attached to their C-termini. To study conformational properties of such loop-containing hybrids it is necessary to produce them in bacteria. In peptides obtained in this way the helix will be destabilized by the negatively charged C-terminal alpha-carboxyl groups. We propose to block them by the homoserine lactone. The results presented in this paper indicate that the presence of the lactone even at the C-terminus of the loop does not have any negative effect on the loop helix-nucleation ability. On the other hand, the presence of the alpha-NH3+ at the loop N-terminus leads to a drop of metal-binding constant and loss of the rigid structure of the alpha-helical segment of the loop. The alpha-amino group separated by one glycine residue from the loop N-terminus should also be avoided because it perturbs the conformation of the N-terminal part of the loop and may reduce the loop affinity to lanthanide ions.

Effects of Metal-Binding Loop Mutations on Ligand Binding to Calcium- and Integrin-Binding Protein 1. Evolution of the EF-Hand?†

Biochemistry ◽  
2008 ◽  
Vol 47 (6) ◽  
pp. 1696-1707 ◽  
Author(s):  
Aaron P. Yamniuk ◽  
Jessica L. Gifford ◽  
Sara Linse ◽  
Hans J. Vogel
Keyword(s):  
Ligand Binding ◽  
Metal Binding ◽  
Binding Protein ◽  
Ef Hand ◽  
Binding Loop

A NEW FUNCTION OF HUMAN KININOGENS: THE AMINO-TERMINAL REGION OF DOMAIN 1 INVOLVES AN EF HAND-LIKE STRACTURE FOR METAL BINDING

1987 ◽  
Author(s):  
S Higashiyama ◽  
I Ohkubo ◽  
H Ishiguro ◽  
M Sasaki
Keyword(s):  
Molecular Weight ◽  
Conformational Changes ◽  
Heavy Chain ◽  
Metal Binding ◽  
Cysteine Proteinase ◽  
Coagulation Cascade ◽  
Cysteine Proteinase Inhibitor ◽  
Amino Terminal ◽  
Ef Hand ◽  
Cnbr Cleavage

Two types of kininogens in mammalian plasma, high molecular weight (HMW) and low molecular weight (LMW) kininogens, are the precursors of kinin. Especially, HMW kininogen circulates in the plasma as a complex with prekallikrein and factor XI, and functions as a cofactor in the initial phase reactions of intrinsic blood coagulation cascade. Recently, it has been found that the kininogens have inhibitory activity toward cysteine proteinases. The heavy chain portion, which is identical for HMW and LMW kininogens, is composed of three domains, domain 1, 2 and 3. Each the domain 2 and 3 has a reactive site as a cysteine proteinase inhibitor. However, physiological function of domain 1 remains still unknown. By using the antibody recognizing the interaction between HMW kininogen and Ca2+ (anti-HMW kininogen-Ca2+ antibody) as a probe, we newly found the Ca2+ binding site in the domain 1.Anti-HMW kininogen-Ca2+ antibody was isolated from anti-HMW kininogen antiserum as an antibody which bound to a HMW kininogen-Sepharose column equilibrated with 40 mM Tris-HCl buffer, pH 7.5, containing 1.0 M NaCl and 1 mM CaCl2, and was eluted with 3 mM EDTA. Resulting from the characterization by ELISA, this antibody specifically recognized the CB-1 region (CNBr-cleavage fragment 1: 1-160 amino acid sequence) of the heavy chain of kininogen molecules in the presence of Ca2+ or Mg2+. Furthermore, circular dichroism (CD) experiments showed that the conformational changes of HMW kininogen and heavy chain were induced by the addition of metal ions such as Ca2+ or Mg2+, and that this change was due to the conformational change of the CB-1 region. The dissociation constant (Kd) for heavy chain measured by Ca2+ titration analysis by CD at 214 nm was found to be 0.33 ± 0.09 mM. The number of Ca2+ binding sites of heavy chain calculated from Hill plot was 1.15 ± 0.04. The EF handlike structure found in the amino-terminal portion of the heavy chain of kininogen molecules strongly supported the above data. This indicates a possibility that kininogens play an important role as a Ca2+ binding protein.

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