Structures and metal-ion-binding properties of the Ca2+-binding helix–loop–helix EF-hand motifs

2007 ◽  
Vol 405 (2) ◽  
pp. 199-221 ◽  
Author(s):  
Jessica L. Gifford ◽  
Michael P. Walsh ◽  
Hans J. Vogel
Keyword(s):  
Metal Ion ◽  
Molten Globule ◽  
Family Members ◽  
Binding Motif ◽  
Metal Ion Binding ◽  
Protein Target ◽  
Helix Loop Helix ◽  
Wide Range ◽  
Ef Hand ◽  
Ef Hands

The ‘EF-hand’ Ca2+-binding motif plays an essential role in eukaryotic cellular signalling, and the proteins containing this motif constitute a large and functionally diverse family. The EF-hand is defined by its helix–loop–helix secondary structure as well as the ligands presented by the loop to bind the Ca2+ ion. The identity of these ligands is semi-conserved in the most common (the ‘canonical’) EF-hand; however, several non-canonical EF-hands exist that bind Ca2+ by a different co-ordination mechanism. EF-hands tend to occur in pairs, which form a discrete domain so that most family members have two, four or six EF-hands. This pairing also enables communication, and many EF-hands display positive co-operativity, thereby minimizing the Ca2+ signal required to reach protein saturation. The conformational effects of Ca2+ binding are varied, function-dependent and, in some cases, minimal, but can lead to the creation of a protein target interaction site or structure formation from a molten-globule apo state. EF-hand proteins exhibit various sensitivities to Ca2+, reflecting the intrinsic binding ability of the EF-hand as well as the degree of co-operativity in Ca2+ binding to paired EF-hands. Two additional factors can influence the ability of an EF-hand to bind Ca2+: selectivity over Mg2+ (a cation with very similar chemical properties to Ca2+ and with a cytoplasmic concentration several orders of magnitude higher) and interaction with a protein target. A structural approach is used in this review to examine the diversity of family members, and a biophysical perspective provides insight into the ability of the EF-hand motif to bind Ca2+ with a wide range of affinities.

scholarly journals The Highly Conservative Cysteine of Oncomodulin as a Feasible Redox Sensor

Biomolecules ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 66
Author(s):  
Alisa A. Vologzhannikova ◽  
Polina A. Khorn ◽  
Marina P. Shevelyova ◽  
Alexei S. Kazakov ◽  
Victor I. Emelyanenko ◽  
...  
Keyword(s):  
Solvent Accessibility ◽  
Sensory Function ◽  
Hydrophobic Residues ◽  
Metal Free ◽  
Helix Loop Helix ◽  
Redox Sensor ◽  
Ef Hand ◽  
Functional Consequences ◽  
Ef Hands ◽  
Ph Range

Oncomodulin (Ocm), or parvalbumin β, is an 11–12 kDa Ca2+-binding protein found inside and outside of vertebrate cells, which regulates numerous processes via poorly understood mechanisms. Ocm consists of two active Ca2+-specific domains of the EF-hand type (“helix-loop-helix” motif), covered by an EF-hand domain with inactive EF-hand loop, which contains a highly conservative cysteine with unknown function. In this study, we have explored peculiarities of the microenvironment of the conservative Cys18 of recombinant rat Ocm (rWT Ocm), redox properties of this residue, and structural/functional sensitivity of rWT Ocm to the homologous C18S substitution. We have found that pKa of the Cys18 thiol lays beyond the physiological pH range. The measurement of redox dependence of rWT Ocm thiol–disulfide equilibrium (glutathione redox pair) showed that redox potential of Cys18 for the metal-free and Ca2+-loaded protein is of −168 mV and −176 mV, respectively. Therefore, the conservative thiol of rWT Ocm is prone to disulfide dimerization under physiological redox conditions. The C18S substitution drastically reduces α-helices content of the metal-free and Mg2+-bound Ocm, increases solvent accessibility of its hydrophobic residues, eliminates the cooperative thermal transition in the apo-protein, suppresses Ca2+/Mg2+ affinity of the EF site, and accelerates Ca2+ dissociation from Ocm. The distinct structural and functional consequences of the minor structural modification of Cys18 indicate its possible redox sensory function. Since some other EF-hand proteins also contain a conservative redox-sensitive cysteine located in an inactive EF-hand loop, it is reasonable to suggest that in the course of evolution, some of the EF-hands attained redox sensitivity at the expense of the loss of their Ca2+ affinity.

scholarly journals Calcium(II) site specificity: effect of size and charge on metal ion binding to an EF-hand-like site

Biochemistry ◽  
1990 ◽  
Vol 29 (16) ◽  
pp. 3937-3943 ◽  
Author(s):  
Eric E. Snyder ◽  
Brian W. Buoscio ◽  
Joseph J. Falke
Keyword(s):  
Metal Ion ◽  
Ion Binding ◽  
Site Specificity ◽  
Metal Ion Binding ◽  
Ef Hand ◽  
Specificity Effect

GLOBAL METAL-ION BINDING PROTEIN FINGERPRINT: A METHOD TO IDENTIFY MOTIF-LESS METAL-ION BINDING PROTEINS

2010 ◽  
Vol 08 (04) ◽  
pp. 717-726 ◽  
Author(s):  
ABHILASH MOHAN ◽  
SHARMILA ANISHETTY ◽  
PENNATHUR GAUTAM
Keyword(s):  
Metal Ion ◽  
Binding Proteins ◽  
Binding Protein ◽  
Vital Role ◽  
Ion Binding ◽  
Binding Motif ◽  
Specific Class ◽  
Metal Ion Binding ◽  
Knowledge Based ◽  
Supervised Classifiers

Metal-ion binding proteins play a vital role in biological processes. Identifying putative metal-ion binding proteins is through knowledge-based methods. These involve the identification of specific motifs that characterize a specific class of metal-ion binding protein. Metal-ion binding motifs have been identified for the common metal ions. A robust global fingerprint that is useful in identifying a metal-ion binding protein from a non-metal-ion binding protein has not been devised. Such a method will help in identifying novel metal-ion binding proteins and proteins that do not possess a canonical metal-ion binding motif. We have used a set of physico-chemical parameters of metal-ion binding proteins encoded by the genes CzcA, CzcB and CzcD as a training set to supervised classifiers and have been able to identify several other metal ion binding proteins leading us to believe that metal-ion binding proteins have a global fingerprint, which cannot be pinned down to a single feature of the protein sequence.

scholarly journals Amyloid Assembly Endows Gad m 1 with Biomineralization Properties

2018 ◽  
Author(s):  
Milagros Castellanos ◽  
Rosa Rodríguez-Pérez ◽  
María Gasset
Keyword(s):  
Calcium Carbonate ◽  
Atlantic Cod ◽  
Fish Muscle ◽  
Binding Motif ◽  
Beta Strand ◽  
Ef Hand ◽  
Acidic Conditions ◽  
Ef Hands ◽  
Amyloid Assembly

Acid proteins capable of nucleating Ca2+ and displaying aggregation capacity play key roles in the formation of calcium carbonate biominerals. EF-hands are among the largest Ca2+-binding motif in proteins. Gad m 1, an Atlantic cod β-parvalbumin isoform, is a monomeric EF-hand protein that acts as a Ca2+ buffer in fish muscle and is able to form amyloids under acidic conditions. Since nucleating Ca2+ protein have a propensity to form extended β-strand structures, we wondered whether amyloid assemblies of a protein containing refolded EF-hand motifs were able to influence the in vitro calcium carbonate crystallization. Here we have used the Gad m 1 chain as model to generate monomeric and amyloid assemblies and analyze their effect on in vitro calcite formation. We found that only amyloid assemblies alter calcite morphology.

scholarly journals Conserved properties of individual Ca2+-binding sites in calmodulin

2016 ◽  
Vol 113 (9) ◽  
pp. E1216-E1225 ◽  
Author(s):  
D. Brent Halling ◽  
Benjamin J. Liebeskind ◽  
Amelia W. Hall ◽  
Richard W. Aldrich
Keyword(s):  
Binding Sites ◽  
Evolutionary Analysis ◽  
Dependent Manner ◽  
Target Proteins ◽  
Wide Range ◽  
Ef Hand ◽  
Life Threatening ◽  
Ef Hands ◽  
Future Work ◽  
The Relationship

Calmodulin (CaM) is a Ca2+-sensing protein that is highly conserved and ubiquitous in eukaryotes. In humans it is a locus of life-threatening cardiomyopathies. The primary function of CaM is to transduce Ca2+ concentration into cellular signals by binding to a wide range of target proteins in a Ca2+-dependent manner. We do not fully understand how CaM performs its role as a high-fidelity signal transducer for more than 300 target proteins, but diversity among its four Ca2+-binding sites, called EF-hands, may contribute to CaM’s functional versatility. We therefore looked at the conservation of CaM sequences over deep evolutionary time, focusing primarily on the four EF-hand motifs. Expanding on previous work, we found that CaM evolves slowly but that its evolutionary rate is substantially faster in fungi. We also found that the four EF-hands have distinguishing biophysical and structural properties that span eukaryotes. These results suggest that all eukaryotes require CaM to decode Ca2+ signals using four specialized EF-hands, each with specific, conserved traits. In addition, we provide an extensive map of sites associated with target proteins and with human disease and correlate these with evolutionary sequence diversity. Our comprehensive evolutionary analysis provides a basis for understanding the sequence space associated with CaM function and should help guide future work on the relationship between structure, function, and disease.

scholarly journals Interaction of metal ions with glutaminase interacting protein (GIP): A potential role of GIP in brain diseases

2008 ◽  
Vol 22 (4) ◽  
pp. 213-221 ◽  
Author(s):  
Priscilla Ward ◽  
Chengdong Huang ◽  
Monimoy Banerjee ◽  
Smita Mohanty
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Pdz Domain ◽  
Brain Diseases ◽  
Ion Binding ◽  
Signaling System ◽  
Metal Ion Binding ◽  
Interacting Protein ◽  
Glutamate Signaling ◽  
Wide Range

Glutaminase interacting protein (GIP), a PDZ domain containing protein, mediates the distribution and clustering of proteins/peptides in membranes, acting as a scaffold where signaling molecules are linked to a multi-protein complex. GIP has been shown to play a key role in the glutamate signaling system. Some metals, particularly Pb2+, Cu2+and Zn2+, have been implicated in a wide range of neurological disorders including Alzheimer's disease and Parkinson's disease, whose etiologies have been associated with dysfunction of the glutamate signaling system. Here, for the first time, the effects of lead, copper, and zinc on GIP were determined by using circular dichroism and fluorescence spectroscopy. All three metal ions significantly affected the conformational properties of GIP. The deconvolution of CD data showed that, with increasing amounts of Pb2+/Cu2+/Zn2+, theα-helix percentage decreased while theβ-sheet content increased. The binding constants of GIP to Pb2+, Cu2+and Zn2+determined by fluorescence were found to be 1.4, 2.38 and 2.85 μM respectively, which indicated strong bindings between GIP and all three metal ions. We propose that the metal ion binding site of GIP is located onα-2 helix, where residues His90, Asp91 and Arg94 may coordinate the metal ions. The conformational change of GIP upon metal ion binding possibly results from the disruption of a salt bridge between Asp91 and Arg94.

scholarly journals Behavior control of membrane-less protein liquid condensates with metal ion-induced phase separation

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Kibeom Hong ◽  
Daesun Song ◽  
Yongwon Jung
Keyword(s):  
Phase Separation ◽  
Metal Ion ◽  
Liquid Droplet ◽  
Receptor Protein ◽  
Binding Motif ◽  
Receptor Ligand ◽  
Precise Control ◽  
Hexahistidine Tag ◽  
Wide Range ◽  
In Cells

Abstract Phase separation of specific biomolecules into liquid droplet-like condensates is a key mechanism to form membrane-less organelles, which spatio-temporally organize diverse biochemical processes in cells. To investigate the working principles of these biomolecular condensates as dynamic reaction centers, precise control of diverse condensate properties is essential. Here, we design a strategy for metal ion-induced clustering of minimal protein modules to produce liquid protein condensates, the properties of which can be widely varied by simple manipulation of the protein clustering systems. The droplet forming-minimal module contains only a single receptor protein and a binding ligand peptide with a hexahistidine tag for divalent metal ion-mediated clustering. A wide range of protein condensate properties such as droplet forming tendency, droplet morphology, inside protein diffusivity, protein recruitment, and droplet density can be varied by adjusting the nature of receptor/ligand pairs or used metal ions, metal/protein ratios, incubation time, binding motif variation on recruited proteins, and even spacing between receptor/ligand pairs and the hexahistidine tag. We also demonstrate metal-ion-induced protein phase separation in cells. The present phase separation strategy provides highly versatile protein condensates, which will greatly facilitate investigation of molecular and structural codes of droplet-forming proteins and the monitoring of biomolecular behaviors inside diverse protein condensates.

scholarly journals The Xanthomonas RaxH-RaxR Two-Component Regulatory System Is Orthologous to the Zinc-Responsive Pseudomonas ColS-ColR System

2021 ◽  
Vol 9 (7) ◽  
pp. 1458
Author(s):  
Valley Stewart ◽  
Pamela C. Ronald
Keyword(s):  
Metal Ion ◽  
Lipid A ◽  
Regulatory System ◽  
Binding Motif ◽  
Metal Ion Binding ◽  
Sequence Comparisons ◽  
Regulatory Systems ◽  
Two Component ◽  
Periplasmic Domain ◽  
Genome Annotations

Genome sequence comparisons to infer likely gene functions require accurate ortholog assignments. In Pseudomonas spp., the sensor-regulator ColS-ColR two-component regulatory system responds to zinc and other metals to control certain membrane-related functions, including lipid A remodeling. In Xanthomonas spp., three different two-component regulatory systems, RaxH-RaxR, VgrS-VgrR, and DetS-DetR, have been denoted as ColS-ColR in several different genome annotations and publications. To clarify these assignments, we compared the sensor periplasmic domain sequences and found that those from Pseudomonas ColS and Xanthomonas RaxH share a similar size as well as the location of a Glu-X-X-Glu metal ion-binding motif. Furthermore, we determined that three genes adjacent to raxRH are predicted to encode enzymes that remodel the lipid A component of lipopolysaccharide. The modifications catalyzed by lipid A phosphoethanolamine transferase (EptA) and lipid A 1-phosphatase (LpxE) previously were detected in lipid A from multiple Xanthomonas spp. The third gene encodes a predicted lipid A glycosyl transferase (ArnT). Together, these results indicate that the Xanthomonas RaxH-RaxR system is orthologous to the Pseudomonas ColS-ColR system that regulates lipid A remodeling. To avoid future confusion, we recommend that the terms ColS and ColR no longer be applied to Xanthomonas spp., and that the Vgr, Rax, and Det designations be used instead.

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