scholarly journals Roles of individual EF-hands in the activation of m-calpain by calcium

2000 ◽  
Vol 348 (1) ◽  
pp. 37-43 ◽  
Author(s):  
Previn DUTT ◽  
J. C. Simon ARTHUR ◽  
Pawel GROCHULSKI ◽  
Miroslaw CYGLER ◽  
John S. ELCE
Keyword(s):  
Driving Force ◽  
Specific Activity ◽  
Small Subunit ◽  
Wild Type ◽  
X Ray ◽  
X Ray Crystallography ◽  
Kd Values ◽  
Ef Hand ◽  
Ef Hands ◽  
Made In

m-Calpain is a heterodimeric, cytosolic, thiol protease, which is activated by Ca2+-binding to EF-hands in the C-terminal domains of both subunits. There are four potential Ca2+-binding EF-hands in each subunit, but their relative affinities for Ca2+ are not known. In the present study mutations were made in both subunits to reduce the Ca2+-binding affinity at one or more EF-hands in one or both subunits. X-ray crystallography of some of the mutated small subunits showed that Ca2+ did not bind to the mutated EF-hands, but that its binding at other sites was not affected. The structures of the mutant small subunits in the presence of Ca2+ were otherwise identical to that of the Ca2+-bound wild-type small subunit. In the whole enzyme the wild-type macroscopic Ca2+ requirement (Kd) was approx. 350 μM. The mutations did not affect the maximum specific activity of the enzyme, but caused increases in Kd, which were characteristic of each site. All the EF-hands could be mutated in various combinations without loss of activity, but preservation of at least one wild-type EF-hand 3 sequence was required to maintain Kd values lower than 1 mM. The results suggest that all the EF-hands can contribute co-operatively to calpain activation, but that EF-hand 3, in both subunits, has the highest intrinsic affinity for Ca2+ and provides the major driving force for conformational change.

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 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 Mutational analysis of centrin: an EF-hand protein associated with three distinct contractile fibers in the basal body apparatus of Chlamydomonas.

1992 ◽  
Vol 119 (6) ◽  
pp. 1613-1624 ◽  
Author(s):  
B E Taillon ◽  
S A Adler ◽  
J P Suhan ◽  
J W Jarvik
Keyword(s):  
Amino Acid ◽  
Basal Body ◽  
Calcium Binding ◽  
Mutational Analysis ◽  
Structural Defects ◽  
Wild Type ◽  
Immunofluorescence Analysis ◽  
Ef Hand ◽  
Level 1 ◽  
Ef Hands

Centrin, a 20-kD phosphoprotein with four calcium-binding EF-hands, is present in the centrosome/basal body apparatus of the green alga Chlamydomonas reinhardtii in three distinct locations: the nucleus-basal body connectors, the distal striated fibers, and the flagellar transition regions. In each location, centrin is found in fibrous structures that display calcium-mediated contraction. The mutant vfl2 has structural defects at all of these locations and is defective for basal body localization and/or segregation. We show that the vfl2 mutation is a G-to-A transition in the centrin structural gene which converts a glutamic acid to a lysine at position 101, the first amino acid of the E-helix of the protein's third EF-hand. This proves that centrin is required to construct the nucleus-basal body connectors, the distal striated fibers, and the flagellar transition regions, and it demonstrates the importance of amino acid 101 to normal centrin function. Based on immunofluorescence analysis using anti-centrin antibodies, it appears that vfl2 centrin is capable of binding to the basal body but is incapable of polymerizing into filamentous structures. 19 phenotypic revertants of vfl2 were isolated, and 10 of them, each of which had undergone further mutation at codon 101, were examined in detail. At the DNA level, 1 of the 10 was wild type, and the other 9 were pseudorevertants encoding centrins with the amino acids asparagine, threonine, methionine, or isoleucine at position 101. No ultrastructure defects were apparent in the revertants with asparagine or threonine at position 101, but in those with methionine or isoleucine at position 101, the distal striated fibers were found to be incomplete, indicating that different amino acid substitutions at position 101 can differentially affect the assembly of the three distinct centrin-containing fibrous structures associated with the Chlamydomonas centrosome.

scholarly journals Identification and Mutagenesis of the Adeno-Associated Virus 5 Sialic Acid Binding Region

2014 ◽  
Vol 89 (3) ◽  
pp. 1660-1672 ◽  
Author(s):  
Sandra Afione ◽  
Michael A. DiMattia ◽  
Sujata Halder ◽  
Giovanni Di Pasquale ◽  
Mavis Agbandje-McKenna ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Wild Type Virus ◽  
Fold Axis ◽  
Cell Tropism ◽  
Type Virus ◽  
Wild Type ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sialic Acid Binding

ABSTRACTAs a genus, the dependoviruses use a diverse group of cell surface carbohydrates for attachment and entry. Despite the fact that a majority of adeno-associated viruses (AAVs) utilize sialic acid (SIA) for binding and transduction, this virus-carbohydrate interaction is poorly understood. Utilizing X-ray crystallography, two SIA binding regions were mapped for AAV5. The first site mapped to the depression in the center of the 3-fold axis of symmetry, while the second site was located under the βHI loop close to the 5-fold axis. Mutagenesis of amino acids 569 and 585 or 587 within the 3-fold depression resulted in elimination or alteration in SIA-dependent transduction, respectively. This change in SIA binding was confirmed using glycan microarrays. Mutagenesis of the second site identified a role in transduction that was SIA independent. Further studies of the mutants at the 3-fold site demonstrated a change in transduction activity and cell tropismin vivoas well as resistance to neutralization by a polyclonal antibody raised against the wild-type virus.IMPORTANCEDespite the fact that a majority of AAVs utilize sialic acid for binding and transduction, this virus-carbohydrate interaction is poorly understood. Utilizing X-ray crystallography, the sialic acid binding regions of AAV5 were identified and studied using a variety of approaches. Mutagenesis of this region resulted in elimination or alteration in sialic acid-dependent transduction in cell lines. This change in sialic acid glycan binding was confirmed using glycan arrays. Further study also demonstrated a change in transduction and activity and cell tropismin vivoas well as resistance to neutralization by antibodies raised against the wild-type virus.

scholarly journals Orchestrating serine resolvases

2010 ◽  
Vol 38 (2) ◽  
pp. 384-387 ◽  
Author(s):  
Phoebe A. Rice ◽  
Kent. W. Mouw ◽  
Sherwin P. Montaño ◽  
Martin R. Boocock ◽  
Sally-J. Rowland ◽  
...  
Keyword(s):  
Dna Bending ◽  
Strand Exchange ◽  
Wild Type ◽  
Remarkable Feature ◽  
Synaptic Complex ◽  
X Ray ◽  
X Ray Crystallography ◽  
Crossover Site ◽  
Net Release ◽  
Reaction Direction

A remarkable feature of the serine resolvases is their regulation: the wild-type enzymes will catalyse intra- but not inter-molecular recombination, can sense the relative orientation of their sites and can exchange strands directionally, despite the fact that there is no net release of chemical bond energy. The key to this regulation is that they are only active within a large intertwined complex called the ‘synaptosome’. Because substrate topology greatly facilitates (or, in other cases, inhibits) formation of the synaptosome, it acts as a ‘topological filter’. Within the defined topology of the synaptosome, strand exchange releases supercoiling tension, providing an energy source to bias the reaction direction. The regulatory portion of this complex contains additional copies of the recombinase and sometimes other DNA-bending proteins. We are using a combination of X-ray crystallography, biochemistry and genetics to model the full synaptic complex and to understand how the regulatory portion activates the crossover-site-bound recombinases.

scholarly journals PGRP-LB: An Inside View into the Mechanism of the Amidase Reaction

2021 ◽  
Vol 22 (9) ◽  
pp. 4957
Author(s):  
Julien Orlans ◽  
Carole Vincent-Monegat ◽  
Isabelle Rahioui ◽  
Catherine Sivignon ◽  
Agata Butryn ◽  
...  
Keyword(s):  
Specific Activity ◽  
Insect Immunity ◽  
Site Directed Mutagenesis ◽  
Nucleophilic Attack ◽  
Wild Type ◽  
X Ray ◽  
Enzymatic Mechanism ◽  
Imd Pathway ◽  
Essential Function

Peptidoglycan recognition proteins (PGRPs) are ubiquitous among animals and play pivotal functions in insect immunity. Non-catalytic PGRPs are involved in the activation of immune pathways by binding to the peptidoglycan (PGN), whereas amidase PGRPs are capable of cleaving the PGN into non-immunogenic compounds. Drosophila PGRP-LB belongs to the amidase PGRPs and downregulates the immune deficiency (IMD) pathway by cleaving meso-2,6-diaminopimelic (meso-DAP or DAP)-type PGN. While the recognition process is well analyzed for the non-catalytic PGRPs, little is known about the enzymatic mechanism for the amidase PGRPs, despite their essential function in immune homeostasis. Here, we analyzed the specific activity of different isoforms of Drosophila PGRP-LB towards various PGN substrates to understand their specificity and role in Drosophila immunity. We show that these isoforms have similar activity towards the different compounds. To analyze the mechanism of the amidase activity, we performed site directed mutagenesis and solved the X-ray structures of wild-type Drosophila PGRP-LB and its mutants, with one of these structures presenting a protein complexed with the tracheal cytotoxin (TCT), a muropeptide derived from the PGN. Only the Y78F mutation abolished the PGN cleavage while other mutations reduced the activity solely. Together, our findings suggest the dynamic role of the residue Y78 in the amidase mechanism by nucleophilic attack through a water molecule to the carbonyl group of the amide function destabilized by Zn2+.

scholarly journals Adamantane-Functionalized Phthalimide Scaffold: Pathways to Supramolecular Interactions and Drug Discovery

Organics ◽  
2021 ◽  
Vol 2 (4) ◽  
pp. 388-394
Author(s):  
Hamidou Keita
Keyword(s):  
Crystal Structure ◽  
Drug Discovery ◽  
Single Crystal ◽  
Benzene Ring ◽  
Driving Force ◽  
Core Structure ◽  
Supramolecular Interactions ◽  
The Novel ◽  
X Ray ◽  
X Ray Crystallography

Herein, the synthesis of a novel adamantanyl-functionalized phthalimide scaffold is demonstrated. The novel compound could be used as a precursor for various synthetic pathways owing to the generic use of adamantane substituents as the driving force for supramolecular interactions with macrocycles and N-substituted phthalimide derivatives as a core structure in numerous drugs. The adamantanyl-functionalized phthalimide scaffold contains bromide groups on the C4 and C5 positions of the benzene ring, effectively allowing further facile modifications of the scaffold. The structure was fully characterized including single-crystal X-ray crystallography. The crystal structure shows an adamantane moiety at an angle of 115.57(7)° to the phthalimide core, hence sterically freeing the adamantane unit for host–guest interactions.

Conquer by cryo-EM without physically dividing

2021 ◽  
Author(s):  
Gabriel C. Lander ◽  
Robert M. Glaeser
Keyword(s):  
Particle Size ◽  
High Resolution ◽  
Single Particle ◽  
Region Of Interest ◽  
Divide And Conquer ◽  
Particle Sizes ◽  
X Ray ◽  
X Ray Crystallography ◽  
Substantial Progress ◽  
Made In

This mini-review provides an update regarding the substantial progress that has been made in using single-particle cryo-EM to obtain high-resolution structures for proteins and other macromolecules whose particle sizes are smaller than 100 kDa. We point out that establishing the limits of what can be accomplished, both in terms of particle size and attainable resolution, serves as a guide for what might be expected when attempting to improve the resolution of small flexible portions of a larger structure using focused refinement approaches. These approaches, which involve computationally ignoring all but a specific, targeted region of interest on the macromolecules, is known as ‘masking and refining,' and it thus is the computational equivalent of the ‘divide and conquer' approach that has been used so successfully in X-ray crystallography. The benefit of masked refinement, however, is that one is able to determine structures in their native architectural context, without physically separating them from the biological connections that they require for their function. This mini-review also compares where experimental achievements currently stand relative to various theoretical estimates for the smallest particle size that can be successfully reconstructed to high resolution. Since it is clear that a substantial gap still remains between the two, we briefly recap the areas in which further improvement seems possible, both in equipment and in methods.

scholarly journals Structural elements within the methylation loop (residues 112–117) and EF hands III and IV of calmodulin are required for Lys115 trimethylation

1999 ◽  
Vol 340 (2) ◽  
pp. 417-424 ◽  
Author(s):  
Jennifer A. COBB ◽  
Chang-Hoon HAN ◽  
David M. WILLS ◽  
Daniel M. ROBERTS
Keyword(s):  
Single Point ◽  
Point Mutations ◽  
Site Directed Mutagenesis ◽  
Structural Elements ◽  
Nad Kinase ◽  
Wild Type ◽  
Loop Sequence ◽  
Ef Hand ◽  
Single Point Mutations ◽  
Ef Hands

Calmodulin is trimethylated by a specific methyltransferase on Lys115, a residue located in a six amino acid loop (LGEKLT) between EF hands III and IV. To investigate the structural requirements for methylation, domain exchange mutants as well as single point mutations of conserved methylation loop residues (E114A, Glu114 → Ala; L116T, Leu116 → Thr) were generated. E114A and L116T activated cyclic nucleotide phosphodiesterase (PDE) and NAD+ kinase (NADK) similar to wild-type calmodulin, but lost their ability to be methylated. Domain exchange mutants in which EF hand III or IV was replaced by EF hand I or II respectively (CaM1214 and CaM1232 respectively) showed a modest effect on PDE and NADK activation (50 to 100% of wild-type), but calmodulin methylation was abolished. A third domain exchange mutant, CaMEKL, has the methylation loop sequence placed at a symmetrical position between EF hands I and II in the N-terminal lobe [residues QNP(41-43) replaced by EKL]. CaMEKL activated PDE normally, but did not activate NADK. However, CaMEKL retained the ability to bind to NADK and inhibited activation by wild-type calmodulin. Site-directed mutagenesis of single residues showed that Gln41 and Pro43 substitutions had the strongest effect on NADK activation. Additionally, CaMEKL was not methylated, suggesting that the introduction of the methylation loop between EF hands I and II is not adequate for methyltransferase recognition. Overall the data indicate that residues in the methylation loop are essential but not sufficient for methyltransferase recognition, and that additional residues unique to EF hands III and IV are required. Secondly, the QNP sequence in the loop between EF hands I and II is necessary for NADK activation.

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