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.

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 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.

Coupling of ligand binding and dimerization of helix-loop-helix peptides: Spectroscopic and sedimentation analyses of calbindin D9k EF-hands

2002 ◽  
Vol 47 (3) ◽  
pp. 323-333 ◽  
Author(s):  
Karin Julenius ◽  
James Robblee ◽  
Eva Thulin ◽  
Bryan E. Finn ◽  
Robert Fairman ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Helix Loop Helix ◽  
Calbindin D9k ◽  
Ef Hands

scholarly journals DC3, the 21-kDa Subunit of the Outer Dynein Arm-Docking Complex (ODA-DC), Is a Novel EF-Hand Protein Important for Assembly of Both the Outer Arm and the ODA-DC

2003 ◽  
Vol 14 (9) ◽  
pp. 3650-3663 ◽  
Author(s):  
Diane M. Casey ◽  
Kazuo Inaba ◽  
Gregory J. Pazour ◽  
Saeko Takada ◽  
Ken-ichi Wakabayashi ◽  
...  
Keyword(s):  
Troponin C ◽  
Light Chains ◽  
Myosin Light Chains ◽  
Cdna Clones ◽  
Wild Type ◽  
Ef Hand ◽  
Dynein Arms ◽  
Ef Hands ◽  
Flagellar Axoneme ◽  
Chlamydomonas Mutants

The outer dynein arm-docking complex (ODA-DC) is a microtubule-associated structure that targets the outer dynein arm to its binding site on the flagellar axoneme ( Takada et al. 2002 . Mol. Biol. Cell 13, 1015–1029). The ODA-DC of Chlamydomonas contains three proteins, referred to as DC1, DC2, and DC3. We here report the isolation and sequencing of genomic and full-length cDNA clones encoding DC3. The sequence predicts a 21,341 Da protein with four EF-hands that is a member of the CTER (calmodulin, troponin C, essential and regulatory myosin light chains) group and is most closely related to a predicted protein from Plasmodium. The DC3 gene, termed ODA14, is intronless. Chlamydomonas mutants that lack DC3 exhibit slow, jerky swimming because of loss of some but not all outer dynein arms. Some outer doublet microtubules without arms had a “partial” docking complex, indicating that DC1 and DC2 can assemble in the absence of DC3. In contrast, DC3 cannot assemble in the absence of DC1 or DC2. Transformation of a DC3-deletion strain with the wild-type DC3 gene rescued both the motility phenotype and the structural defect, whereas a mutated DC3 gene was incompetent to rescue. The results indicate that DC3 is important for both outer arm and ODA-DC assembly.

scholarly journals Structural and dynamic aspects related to oligomerization of apo SOD1 and its mutants

2009 ◽  
Vol 106 (17) ◽  
pp. 6980-6985 ◽  
Author(s):  
Lucia Banci ◽  
Ivano Bertini ◽  
Mirela Boca ◽  
Vito Calderone ◽  
Francesca Cantini ◽  
...  
Keyword(s):  
Solvent Accessibility ◽  
Structural Disorder ◽  
Free Form ◽  
X Ray Diffraction ◽  
X Ray ◽  
Conformational Variability ◽  
Metal Free ◽  
Loop Regions ◽  
Lateral Sclerosis ◽  
Apo State

The structural and dynamical properties of the metal-free form of WT human superoxide dismutase 1 (SOD1) and its familial amyotrophic lateral sclerosis (fALS)-related mutants, T54R and I113T, were characterized both in solution, through NMR, and in the crystal, through X-ray diffraction. We found that all 3 X-ray structures show significant structural disorder in 2 loop regions that are, at variance, well defined in the fully-metalated structures. Interestingly, the apo state crystallizes only at low temperatures, whereas all 3 proteins in the metalated form crystallize at any temperature, suggesting that crystallization selects one of the most stable conformations among the manifold adopted by the apo form in solution. Indeed, NMR experiments show that the protein in solution is highly disordered, sampling a large range of conformations. The large conformational variability of the apo state allows the free reduced cysteine Cys-6 to become highly solvent accessible in solution, whereas it is essentially buried in the metalated state and the crystal structures. Such solvent accessibility, together with that of Cys-111, accounts for the tendency to oligomerization of the metal-free state. The present results suggest that the investigation of the solution state coupled with that of the crystal state can provide major insights into SOD1 pathway toward oligomerization in relation to fALS.

scholarly journals Functional and structural characterization of allosteric activation of phospholipase Cε by Rap1A

2020 ◽  
Vol 295 (49) ◽  
pp. 16562-16571
Author(s):  
Monita Sieng ◽  
Arielle F. Selvia ◽  
Elisabeth E. Garland-Kuntz ◽  
Jesse B. Hopkins ◽  
Isaac J. Fisher ◽  
...  
Keyword(s):  
Tyrosine Kinases ◽  
Small Gtpases ◽  
Ph Domain ◽  
Hydrophobic Residues ◽  
X Ray Scattering ◽  
Catalytically Active ◽  
Ef Hands ◽  
Β Adrenergic Receptors ◽  
G Protein Coupled ◽  
Phospholipase Cε

Phospholipase Cε (PLCε) is activated downstream of G protein–coupled receptors and receptor tyrosine kinases through direct interactions with small GTPases, including Rap1A and Ras. Although Ras has been reported to allosterically activate the lipase, it is not known whether Rap1A has the same ability or what its molecular mechanism might be. Rap1A activates PLCε in response to the stimulation of β-adrenergic receptors, translocating the complex to the perinuclear membrane. Because the C-terminal Ras association (RA2) domain of PLCε was proposed to the primary binding site for Rap1A, we first confirmed using purified proteins that the RA2 domain is indeed essential for activation by Rap1A. However, we also showed that the PLCε pleckstrin homology (PH) domain and first two EF hands (EF1/2) are required for Rap1A activation and identified hydrophobic residues on the surface of the RA2 domain that are also necessary. Small-angle X-ray scattering showed that Rap1A binding induces and stabilizes discrete conformational states in PLCε variants that can be activated by the GTPase. These data, together with the recent structure of a catalytically active fragment of PLCε, provide the first evidence that Rap1A, and by extension Ras, allosterically activate the lipase by promoting and stabilizing interactions between the RA2 domain and the PLCε core.

scholarly journals Prediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure of Proteins

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Shambhu Malleshappa Gowder ◽  
Jhinuk Chatterjee ◽  
Tanusree Chaudhuri ◽  
Kusum Paul
Keyword(s):  
Tertiary Structure ◽  
Structural Information ◽  
Solvent Accessibility ◽  
Conservation Score ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Data Set ◽  
Hydrophobic Residues ◽  
Monomeric Proteins

The analysis of protein structures provides plenty of information about the factors governing the folding and stability of proteins, the preferred amino acids in the protein environment, the location of the residues in the interior/surface of a protein and so forth. In general, hydrophobic residues such as Val, Leu, Ile, Phe, and Met tend to be buried in the interior and polar side chains exposed to solvent. The present work depends on sequence as well as structural information of the protein and aims to understand nature of hydrophobic residues on the protein surfaces. It is based on the nonredundant data set of 218 monomeric proteins. Solvent accessibility of each protein was determined using NACCESS software and then obtained the homologous sequences to understand how well solvent exposed and buried hydrophobic residues are evolutionarily conserved and assigned the confidence scores to hydrophobic residues to be buried or solvent exposed based on the information obtained from conservation score and knowledge of flanking regions of hydrophobic residues. In the absence of a three-dimensional structure, the ability to predict surface accessibility of hydrophobic residues directly from the sequence is of great help in choosing the sites of chemical modification or specific mutations and in the studies of protein stability and molecular interactions.

scholarly journals EF hands at the N-lobe of calmodulin are required for both SK channel gating and stable SK–calmodulin interaction

2009 ◽  
Vol 134 (4) ◽  
pp. 281-293 ◽  
Author(s):  
Weiyan Li ◽  
David B. Halling ◽  
Amelia W. Hall ◽  
Richard W. Aldrich
Keyword(s):  
Modular Design ◽  
Binding Capacity ◽  
Current Model ◽  
Sk Channels ◽  
Channel Activity ◽  
Wild Type ◽  
Sk Channel ◽  
Ef Hand ◽  
Ef Hands ◽  
Small Conductance

Small conductance calcium-activated potassium (SK) channels respond to intracellular Ca2+ via constitutively associated calmodulin (CaM). Previous studies have proposed a modular design for the interaction between CaM and SK channels. The C-lobe and the linker of CaM are thought to regulate the constitutive binding, whereas the N-lobe binds Ca2+ and gates SK channels. However, we found that coexpression of mutant CaM (E/Q) where the N-lobe has only one functional EF hand leads to rapid rundown of SK channel activity, which can be recovered with exogenously applied wild-type (WT), but not mutant, CaM. Our results suggest that the mutation at the N-lobe EF hand disrupts the stable interaction between CaM and SK channel subunits, such that mutant CaM dissociates from the channel complex when the inside of the membrane is exposed to CaM-free solution. The disruption of the stable interaction does not directly result from the loss of Ca2+-binding capacity because SK channels and WT CaM can stably interact in the absence of Ca2+. These findings question a previous conclusion that CaM where the N-lobe has only one functional EF hand can stably support the gating of SK channels. They cannot be explained by the current model of modular interaction between CaM and SK channels, and they imply a role for N-lobe EF hand residues in binding to the channel subunits. Additionally, we found that a potent enhancer for SK channels, 3-oxime-6,7-dichloro-1H-indole-2,3-dione (NS309), enables the recovery of channel activity with CaM (E/Q), suggesting that NS309 stabilizes the interaction between CaM and SK channels. CaM (E/Q) can regulate Ca2+-dependent gating of SK channels in the presence of NS309, but with a lower apparent Ca2+ affinity than WT CaM.

scholarly journals Metal-Free and Ca2+-Bound Structures of a Multidomain EF-Hand Protein, CBP40, from the Lower Eukaryote Physarum polycephalum

Structure ◽  
2003 ◽  
Vol 11 (1) ◽  
pp. 75-85 ◽  
Author(s):  
Wakana Iwasaki ◽  
Hiroshi Sasaki ◽  
Akio Nakamura ◽  
Kazuhiro Kohama ◽  
Masaru Tanokura
Keyword(s):  
Physarum Polycephalum ◽  
Metal Free ◽  
Ef Hand ◽  
Lower Eukaryote

scholarly journals Identification of a Ca(2+)-binding light chain within Chlamydomonas outer arm dynein

1995 ◽  
Vol 108 (12) ◽  
pp. 3757-3764 ◽  
Author(s):  
S.M. King ◽  
R.S. Patel-King
Keyword(s):  
Heavy Chain ◽  
Light Chain ◽  
Dynein Light Chain ◽  
Binding Studies ◽  
Significant Similarity ◽  
Helix Loop Helix ◽  
Ef Hand ◽  
Chain Sequence

We describe here the molecular cloning of the M(r) 18,000 dynein light chain from the outer arm of Chlamydomonas flagella. In vivo, this molecule is directly associated with the gamma dynein heavy chain. Sequence analysis indicates that this light chain is a novel member of the calmodulin superfamily of Ca2+ binding regulatory proteins; this molecule is 42, 37 and 36% identical to calmodulin, centrin/caltractin and troponin C, respectively, and also shows significant similarity to myosin light chains. Although four helix-loop-helix elements are evident, only two conform precisely to the EF hand consensus and are therefore predicted to bind Ca2+ in vivo. In vitro Ca2+ binding studies indicate that this dynein light chain (expressed as a C-terminal fusion with maltose binding protein) has at least one functional Ca2+ binding site with an apparent affinity for Ca2+ of approximately 3 × 10(−5) M. Within the Chlamydomonas flagellum, the transition from an assymmetric to a symmetric waveform (which implies an alteration in dynein activity) is mediated by an increase in intraflagellar Ca2+ from 10(−6) to 10(−1) M; this transition is altered in mutants that lack the outer arm. The data presented here suggest that a Ca(2+)-dependent alteration in the interaction of this dynein light chain with the motor containing heavy chain may affect outer arm function during flagellar reversal.

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