Functional asymmetry in cohesin binding belies inherent symmetry of the dockerin module: insight into cellulosome assembly revealed by systematic mutagenesis

2008 ◽  
Vol 410 (2) ◽  
pp. 331-338 ◽  
Author(s):  
Alon Karpol ◽  
Yoav Barak ◽  
Raphael Lamed ◽  
Yuval Shoham ◽  
Edward A. Bayer
Keyword(s):  
Calcium Binding ◽  
Striking Similarity ◽  
Type I ◽  
Single Mutation ◽  
High Affinity ◽  
Ef Hand ◽  
Repeated Motifs ◽  
Insight Into ◽  
Binding Loop

The cellulosome is an intricate multi-enzyme complex, known for its efficient degradation of recalcitrant cellulosic substrates. Its supramolecular architecture is determined by the high-affinity intermodular cohesin–dockerin interaction. The dockerin module comprises a calcium-binding, duplicated ‘F-hand’ loop–helix motif that bears striking similarity to the EF-hand loop–helix–loop motif of eukaryotic calcium-binding proteins. In the present study, we demonstrate by progressive truncation and alanine scanning of a representative type-I dockerin module from Clostridium thermocellum, that only one of the repeated motifs is critical for high-affinity cohesin binding. The results suggest that the near-symmetry in sequence and structure of the repeated elements of the dockerin is not essential to cohesin binding. The first calcium-binding loop can be deleted entirely, with almost full retention of binding. Likewise, significant deletion of the second repeated segment can be achieved, provided that its calcium-binding loop remains intact. Essentially the same conclusion was verified by systematically mutating the highly conserved residues in the calcium-binding loop. Mutations in one of the calcium-binding loops failed to disrupt cohesin recognition and binding, whereas a single mutation in both loops served to reduce the affinity significantly. The results are mutually compatible with recent crystal structures of the type-I cohesin–dockerin heterodimer, which demonstrate that the dockerin can bind in an equivalent manner to its cohesin counterpart through either its first or second repeated motif. The observed plasticity in cohesin–dockerin binding may facilitate cellulosome assembly in vivo or, alternatively, provide a conformational switch that promotes access of the tethered cellulosomal enzymes to their polysaccharide substrates.

scholarly journals Engineering Competitive Magnesium Binding into the First EF-hand of Skeletal Troponin C

2002 ◽  
Vol 277 (51) ◽  
pp. 49716-49726 ◽  
Author(s):  
Jonathan P. Davis ◽  
Jack A. Rall ◽  
Peter J. Reiser ◽  
Lawrence B. Smillie ◽  
Svetlana B. Tikunova
Keyword(s):  
Calcium Binding ◽  
Psoas Muscle ◽  
Calcium Sensitivity ◽  
Troponin C ◽  
Regulatory Domain ◽  
Calcium Dependent ◽  
High Affinity ◽  
Magnesium Binding ◽  
Ef Hand ◽  
Binding Loop

The goal of this study was to examine the mechanism of magnesium binding to the regulatory domain of skeletal troponin C (TnC). The fluorescence of Trp29, immediately preceding the first calcium-binding loop in TnCF29W, was unchanged by addition of magnesium, but increased upon calcium binding with an affinity of 3.3 μm. However, the calcium-dependent increase in TnCF29Wfluorescence could be reversed by addition of magnesium, with a calculated competitive magnesium affinity of 2.2 mm. When a Z acid pair was introduced into the first EF-hand of TnCF29W, the fluorescence of G34DTnCF29Wincreased upon addition of magnesium or calcium with affinities of 295 and 1.9 μm, respectively. Addition of 3 mmmagnesium decreased the calcium sensitivity of TnCF29Wand G34DTnCF29W∼2- and 6-fold, respectively. Exchange of G34DTnCF29Winto skinned psoas muscle fibers decreased fiber calcium sensitivity ∼1.7-fold compared with TnCF29Wat 1 mm[magnesium]freeand ∼3.2-fold at 3 mm[magnesium]free. Thus, incorporation of a Z acid pair into the first EF-hand allows it to bind magnesium with high affinity. Furthermore, the data suggests that the second EF-hand, but not the first, of TnC is responsible for the competitive magnesium binding to the regulatory domain.

scholarly journals Structure and Identification of Solenin: A Novel Fibrous Protein from BivalveSolen grandisLigament

2014 ◽  
Vol 2014 ◽  
pp. 1-7
Author(s):  
Jun Meng ◽  
Gang-Sheng Zhang ◽  
Zeng-Qiong Huang
Keyword(s):  
Mechanical Performance ◽  
Type I ◽  
Fibrous Proteins ◽  
Repeat Sequences ◽  
Fibrous Protein ◽  
Secondary Structure Analysis ◽  
Solen Grandis ◽  
Opening And Closing ◽  
Insight Into

Fibrous proteins, which derived from natural sources, have been acting as templates for the production of new materials for decades, and most of them have been modified to improve mechanical performance. Insight into the structures of fibrous proteins is a key step for fabricating of bioinspired materials. Here, we revealed the microstructure of a novel fibrous protein: solenin fromSolen grandisligament and identified the protein by MALDI-TOF-TOF-MS and LC-MS-MS analyses. We found that the protein fiber has no hierarchical structure and is homologous to keratin type II cytoskeletal 1 and type I cytoskeletal 9-like, containing “SGGG,” “SYGSGGG,” “GS,” and “GSS” repeat sequences. Secondary structure analysis by FTIR shows that solenin is composed of 41.8%β-sheet, 16.2%β-turn, 26.5%α-helix, and 9.8% disordered structure. We believe that theβ-sheet structure and those repeat sequences which form “glycine loops” may give solenin excellence elastic and flexible properties to withstand tensile stress caused by repeating opening and closing of the shell valves in vivo. This paper contributes a novel fibrous protein for the protein materials world.

A change-in-hand mechanism for S100 signalling

1998 ◽  
Vol 76 (2-3) ◽  
pp. 324-333 ◽  
Author(s):  
Steven P Smith ◽  
Gary S Shaw
Keyword(s):  
Conformational Change ◽  
Calcium Ion ◽  
Calcium Binding ◽  
Binding Proteins ◽  
Three Dimensional ◽  
Calcium Binding Proteins ◽  
C Terminus ◽  
Ef Hand ◽  
Sensor Proteins ◽  
Binding Loop

S100 proteins are a group of small dimeric calcium-binding proteins making up a large subclass of the EF-hand family of calcium-binding proteins. Members of this family of proteins have been proposed to act as intracellular calcium modulatory proteins in a fashion analogous to that of the EF-hand sensor proteins troponin-C and calmodulin. Recently, NMR spectroscopy has provided the three-dimensional structures of the S100 family members S100A6 and S100B in both the apo- and calcium-bound forms. These structures have allowed for the identification of a novel calcium-induced conformational change termed the change-in-hand mechanism. Helix III of the C-terminal calcium-binding loop changes its helix-helix interactions (or handness) with the remainder of the molecule primarily owing to the reorientation of the backbone in an effort to coordinate the calcium ion. This reorientation of helix III exposes several residues in the C-terminus and linker regions of S100B resulting in the formation of a hydrophobic patch surrounded be a number of acidic residues. This site is the proposed region for protein-protein recognition.Key words: S100, calcium-binding protein, EF-hand, conformational change.

scholarly journals A mysterious family of calcium-binding proteins from parasitic worms

2016 ◽  
Vol 44 (4) ◽  
pp. 1005-1010 ◽  
Author(s):  
Charlotte M. Thomas ◽  
David J. Timson
Keyword(s):  
Calcium Ions ◽  
Calcium Binding ◽  
Cell Biology ◽  
Fasciola Hepatica ◽  
Family Members ◽  
Ion Concentration ◽  
Pharmacological Significance ◽  
Ef Hand ◽  
Parasitic Worms

There is a family of proteins from parasitic worms which combine N-terminal EF-hand domains with C-terminal dynein light chain-like domains. Data are accumulating on the biochemistry and cell biology of these proteins. However, little is known about their functions in vivo. Schistosoma mansoni expresses 13 family members (SmTAL1–SmTAL13). Three of these (SmTAL1, SmTAL2 and SmTAL3) have been subjected to biochemical analysis which demonstrated that they have different molecular properties. Although their overall folds are predicted to be similar, small changes in the EF-hand domains result in differences in their ion binding properties. Whereas SmTAL1 and SmTAL2 are able to bind calcium (and some other) ions, SmTAL3 appears to be unable to bind any divalent cations. Similar biochemical diversity has been seen in the CaBP proteins from Fasciola hepatica. Four family members are known (FhCaBP1–4). All of these bind to calcium ions. However, FhCaBP4 dimerizes in the presence of calcium ions, FhCaBP3 dimerizes in the absence of calcium ions and FhCaBP2 dimerizes regardless of the prevailing calcium ion concentration. In both the SmTAL and FhCaBP families, the proteins also differ in their ability to bind calmodulin antagonists and related drugs. Interestingly, SmTAL1 interacts with praziquantel (the drug of choice for treating schistosomiasis). The pharmacological significance (if any) of this finding is unknown.

scholarly journals IL-12 and type I interferon prolong the division of activated CD8 T cells by maintaining high-affinity IL-2 signaling in vivo

2013 ◽  
Vol 211 (1) ◽  
pp. 105-120 ◽  
Author(s):  
Gabriel R. Starbeck-Miller ◽  
Hai-Hui Xue ◽  
John T. Harty
Keyword(s):  
T Cells ◽  
T Cell ◽  
Cd8 T Cells ◽  
Cd8 T Cell ◽  
Type I ◽  
Type I Ifn ◽  
Cellular Division ◽  
High Affinity ◽  
Cell Accumulation

TCR ligation and co-stimulation induce cellular division; however, optimal accumulation of effector CD8 T cells requires direct inflammatory signaling by signal 3 cytokines, such as IL-12 or type I IFNs. Although in vitro studies suggest that IL-12/type I IFN may enhance T cell survival or early proliferation, the mechanisms underlying optimal accumulation of CD8 T cells in vivo are unknown. In particular, it is unclear if disparate signal 3 cytokines optimize effector CD8 T cell accumulation by the same mechanism and how these inflammatory cytokines, which are transiently produced early after infection, affect T cell accumulation many days later at the peak of the immune response. Here, we show that transient exposure of CD8 T cells to IL-12 or type I IFN does not promote survival or confer an early proliferative advantage in vivo, but rather sustains surface expression of CD25, the high-affinity IL-2 receptor. This prolongs division of CD8 T cells in response to basal IL-2, through activation of the PI3K pathway and expression of FoxM1, a positive regulator of cell cycle progression genes. Thus, signal 3 cytokines use a common pathway to optimize effector CD8 T cell accumulation through a temporally orchestrated sequence of cytokine signals that sustain division rather than survival.

scholarly journals Early Postnatal Death and Motor Disorders in Mice Congenitally Deficient in Calnexin Expression

2002 ◽  
Vol 22 (21) ◽  
pp. 7398-7404 ◽  
Author(s):  
Angela Denzel ◽  
Maurizio Molinari ◽  
Cesar Trigueros ◽  
Joanne E. Martin ◽  
Shanti Velmurgan ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Gene Knockout ◽  
Nerve Fibers ◽  
Motor Disorders ◽  
Type I ◽  
Myelinated Nerve ◽  
Gene Knockout Mice ◽  
Deficient Mice ◽  
Insight Into

ABSTRACT Calnexin is a ubiquitously expressed type I membrane protein which is exclusively localized in the endoplasmic reticulum (ER). In mammalian cells, calnexin functions as a chaperone molecule and plays a key role in glycoprotein folding and quality control within the ER by interacting with folding intermediates via their monoglucosylated glycans. In order to gain more insight into the physiological roles of calnexin, we have generated calnexin gene-deficient mice. Despite its profound involvement in protein folding, calnexin is not essential for mammalian-cell viability in vivo: calnexin gene knockout mice were carried to full term, although 50% died within 48 h and the majority of the remaining mice had to be sacrificed within 4 weeks, with only a very few mice surviving to 3 months. Calnexin gene-deficient mice were smaller than their littermates and showed very obvious motor disorders, associated with a dramatic loss of large myelinated nerve fibers. Thus, the critical contribution of calnexin to mammalian physiology is tissue specific.

scholarly journals A systematic genome-wide account of binding sites for the model transcription factor Gcn4

2021 ◽  
pp. gr.276080.121
Author(s):  
Christopher T Coey ◽  
David J. Clark
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Binding Sites ◽  
Yeast Genome ◽  
High Affinity ◽  
First Approximation ◽  
Genome Wide ◽  
Insight Into

Sequence-specific DNA-binding transcription factors are central to gene regulation. They are often associated with consensus binding sites that predict far more genomic sites than are bound in vivo. One explanation is that most sites are blocked by nucleosomes, such that only sites in nucleosome-depleted regulatory regions are bound. We compared the binding of the yeast transcription factor Gcn4 in vivo using published ChIP-seq data (546 sites) and in vitro, using a modified SELEX method ("G-SELEX"), which utilizes short genomic DNA fragments to quantify binding at all sites. We confirm that Gcn4 binds strongly to an AP-1-like sequence (TGACTCA) and weakly to half-sites. However, Gcn4 binds only some of the 1078 exact matches to this sequence, even in vitro. We show that there are only 166 copies of the high-affinity RTGACTCAY site (exact match) in the yeast genome, all occupied in vivo, largely independently of whether they are located in nucleosome-depleted or nucleosomal regions. Generally, RTGACTCAR/YTGACTCAY sites are bound much more weakly and YTGACTCAR sites are unbound, with biological implications for determining induction levels. We conclude that, to a first approximation, Gcn4 binding can be predicted using the high-affinity site, without reference to chromatin structure. We propose that transcription factor binding sites should be defined more precisely using quantitative data, allowing more accurate genome-wide prediction of binding sites and greater insight into gene regulation.

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 Calcium-dependent and -independent interactions of the S100 protein family

2006 ◽  
Vol 396 (2) ◽  
pp. 201-214 ◽  
Author(s):  
Liliana Santamaria-Kisiel ◽  
Anne C. Rintala-Dempsey ◽  
Gary S. Shaw
Keyword(s):  
Protein Interactions ◽  
Calcium Binding ◽  
S100 Protein ◽  
Cytoskeletal Proteins ◽  
S100 Proteins ◽  
Target Proteins ◽  
Calcium Dependent ◽  
Ef Hand

The S100 proteins comprise at least 25 members, forming the largest group of EF-hand signalling proteins in humans. Although the proteins are expressed in many tissues, each S100 protein has generally been shown to have a preference for expression in one particular tissue or cell type. Three-dimensional structures of several S100 family members have shown that the proteins assume a dimeric structure consisting of two EF-hand motifs per monomer. Calcium binding to these S100 proteins, with the exception of S100A10, results in an approx. 40° alteration in the position of helix III, exposing a broad hydrophobic surface that enables the S100 proteins to interact with a variety of target proteins. More than 90 potential target proteins have been documented for the S100 proteins, including the cytoskeletal proteins tubulin, glial fibrillary acidic protein and F-actin, which have been identified mostly from in vitro experiments. In the last 5 years, efforts have concentrated on quantifying the protein interactions of the S100 proteins, identifying in vivo protein partners and understanding the molecular specificity for target protein interactions. Furthermore, the S100 proteins are the only EF-hand proteins that are known to form both homo- and hetero-dimers, and efforts are underway to determine the stabilities of these complexes and structural rationales for their formation and potential differences in their biological roles. This review highlights both the calcium-dependent and -independent interactions of the S100 proteins, with a focus on the structures of the complexes, differences and similarities in the strengths of the interactions, and preferences for homo- compared with hetero-dimeric S100 protein assembly.

scholarly journals Combination PPARγand RXR Agonist Treatment in Melanoma Cells: Functional Importance of S100A2

PPAR Research ◽  
2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Joshua P. Klopper ◽  
Vibha Sharma ◽  
Reid Bissonnette ◽  
Bryan R. Haugen
Keyword(s):  
Calcium Binding ◽  
Hormone Receptors ◽  
Amelanotic Melanoma ◽  
Antiproliferative Effects ◽  
Over Expression ◽  
Poorly Differentiated ◽  
Insight Into ◽  
Synergistic Increase

Nuclear hormone receptors, including RXR and PPARγ, represent novel therapeutic targets in melanoma. We have previously shown that the DRO subline of the amelanotic melanoma A375 responds to rexinoid and thiazolidinedione (TZD) treatmentin vitroandin vivo. We performed microarray analysis of A375(DRO) after TZD and combination rexinoid/TZD treatment in which the calcium binding protein S100A2 had increased expression after rexinoid or TZD treatment and a synergistic increase to combination treatment. Increased S100A2 expression is dependent on an intact PPARγreceptor, but it is not sufficient to mediate the antiproliferative effects of rexinoid/TZD treatment. Over expression of S100A2 enhanced the effect of rexinoid and TZD treatment while inhibition of S100A2 expression attenuated the response to rexinoid/TZD treatment, suggesting that S100A2 is necessary for optimal response to RXR and PPARγactivation by respective ligands. In summary, we have identified potential downstream mediators of rexinoid and TZD treatment in a poorly differentiated melanoma and found that alterations in S100A2 expression affect RXR and PPARγsignaling in A375(DRO) cells. These studies provide insight into potential mechanisms of tumor response or resistance to these novel therapies.

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