scholarly journals CriTER-A: A Novel Temperature-Dependent Noncoding RNA Switch in the Telomeric Transcriptome of Chironomus riparius

2021 ◽  
Vol 22 (19) ◽  
pp. 10310
Author(s):  
Cristina Romero-López ◽  
Alfredo Berzal-Herranz ◽  
José Luis Martínez-Guitarte ◽  
Mercedes de la Fuente
Keyword(s):  
Thermal Stress ◽  
Noncoding Rna ◽  
Relative Proportion ◽  
Chironomus Riparius ◽  
Temperature Dependent ◽  
Differential Behaviour ◽  
High Sequence Homology ◽  
Function Relationship ◽  
Relationship Of

The telomeric transcriptome of Chironomus riparius has been involved in thermal stress response. One of the telomeric transcripts, the so-called CriTER-A variant, is highly overexpressed upon heat shock. On the other hand, its homologous variant CriTER-B, which is the most frequently encoded noncoding RNA in the telomeres of C. riparius, is only slightly affected by thermal stress. Interestingly, both transcripts show high sequence homology, but less is known about their folding and how this could influence their differential behaviour. Our study suggests that CriTER-A folds as two different conformers, whose relative proportion is influenced by temperature conditions. Meanwhile, the CriTER-B variant shows only one dominant conformer. Thus, a temperature-dependent conformational equilibrium can be established for CriTER-A, suggesting a putative functional role of the telomeric transcriptome in relation to thermal stress that could rely on the structure–function relationship of the CriTER-A transcripts.

Role of aromatic residues in the structure-function relationship of .alpha.-bungarotoxin

Biochemistry ◽  
1982 ◽  
Vol 21 (11) ◽  
pp. 2592-2600 ◽  
Author(s):  
Yee Hsiung Chen ◽  
Jang Chyi Tai ◽  
Wan Jen Huang ◽  
Ming Zong Lai ◽  
Mien Chie Hung ◽  
...  
Keyword(s):  
Structure Function ◽  
Aromatic Residues ◽  
Structure Function Relationship ◽  
Function Relationship ◽  
Alpha Bungarotoxin ◽  
Relationship Of

Uncovering the ultrastructure of ramiform pits in the parenchyma cells of bamboo [Phyllostachys edulis (Carr.) J. Houz.]

Holzforschung ◽  
2020 ◽  
Vol 74 (3) ◽  
pp. 321-331 ◽  
Author(s):  
Caiping Lian ◽  
Shuqin Zhang ◽  
Xianmiao Liu ◽  
Junji Luo ◽  
Feng Yang ◽  
...  
Keyword(s):  
Environmental Scanning Electron Microscopy ◽  
Environmental Scanning ◽  
Type I ◽  
Aperture Diameter ◽  
Parenchyma Cells ◽  
Vascular Parenchyma ◽  
Function Relationship ◽  
Relationship Of ◽  
Important Evidence

AbstractPits are the main transverse channels of intercellular liquid transport in bamboo. Ramiform pits are a special type of simple pit with two or more branches. However, little is known about the morphology and physiological functions of ramiform pits. The anatomy of plants can provide important evidence for the role of cells. To better understand the ultrastructure and the structure-function relationship of ramiform pits, their characteristics need to be investigated. In this study, both qualitative and quantitative features of ramiform pits were studied using field-emission environmental scanning electron microscopy (FE-ESEM). The samples included the native structures and the replica structures obtained by resin castings. The results show that the ramiform pits have a diverse morphology that can be divided into main categories: type I (the primary branches) and type II (the secondary branches). The distribution of ramiform pits is different in ground parenchyma cells (GPCs) and vascular parenchyma cells (VPCs). The number, the pit aperture diameter and the pit canal length of ramiform pits in the VPCs were, respectively, greater (3-fold), larger (2–3-fold) and shorter (1.3-fold) than those in the GPCs.

scholarly journals The Role of the Fibronectin IGD Motif in Stimulating Fibroblast Migration

2007 ◽  
Vol 282 (49) ◽  
pp. 35530-35535 ◽  
Author(s):  
Christopher J. Millard ◽  
Ian R. Ellis ◽  
Andrew R. Pickford ◽  
Ana M. Schor ◽  
Seth L. Schor ◽  
...  
Keyword(s):  
Fibroblast Migration ◽  
Wide Range ◽  
Migration Stimulating Factor ◽  
Function Relationship ◽  
Relationship Of ◽  
Stimulating Factor ◽  
Insight Into ◽  
Stimulation Of

The motogenic activity of migration-stimulating factor, a truncated isoform of fibronectin (FN), has been attributed to the IGD motifs present in its FN type 1 modules. The structure-function relationship of various recombinant IGD-containing FN fragments is now investigated. Their structure is assessed by solution state NMR and their motogenic ability tested on fibroblasts. Even conservative mutations in the IGD motif are inactive or have severely reduced potency, while the structure remains essentially the same. A fragment with two IGD motifs is 100 times more active than a fragment with one and up to 106 times more than synthetic tetrapeptides. The wide range of potency in different contexts is discussed in terms of cryptic FN sites and cooperativity. These results give new insight into the stimulation of fibroblast migration by IGD motifs in FN.

scholarly journals Dynamics-function relationship of N-terminal acetyltransferases: the β6β7 loop modulates substrate accessibility to the catalytic site

2018 ◽  
Author(s):  
Angèle Abboud ◽  
Pierre Bédoucha ◽  
Jan Byška ◽  
Thomas Arnesen ◽  
Nathalie Reuter
Keyword(s):  
Normal Mode Analysis ◽  
Network Models ◽  
Catalytic Site ◽  
Mode Analysis ◽  
Ligand Specificity ◽  
Hairpin Loop ◽  
Domains Of Life ◽  
Function Relationship ◽  
Relationship Of

N-terminal acetyltransferases (NATs) are enzymes catalysing the transfer of the acetyl from Ac-CoA to the N-terminus of proteins, one of the most common protein modifications. Unlike NATs, lysine acetyltransferases (KATs) transfer an acetyl onto the amine group of internal lysines. To date, not much is known on the exclusive substrate specificity of NATs towards protein N-termini. All the NATs and some KATs share a common fold called GNAT. The main difference between NATs and KATs is an extra hairpin loop found only in NATs called β6β7 loop. It covers the active site as a lid. The hypothesized role of the loop is that of a barrier restricting the access to the catalytic site and preventing acetylation of internal lysines. We investigated the dynamics-function relationships of all available structures of NATs covering the three domains of life. Using elastic network models and normal mode analysis, we found a common dynamics pattern conserved through the GNAT fold; a rigid V-shaped groove, formed by the β4 and β5 strands and three relatively more dynamic loops α1α2, β3β4 and β6β7. We identified two independent dynamical domains in the GNAT fold, which is split at the β5 strand. We characterized the β6β7 hairpin loop slow dynamics and show that its movements are able to significantly widen the mouth of the ligand binding site thereby influencing its size and shape. Taken together our results show that NATs may have access to a broader ligand specificity range than anticipated.

Full-length galectin-8 and separate carbohydrate recognition domains: the whole is greater than the sum of its parts?

2020 ◽  
Vol 48 (3) ◽  
pp. 1255-1268
Author(s):  
Alejandro J. Cagnoni ◽  
María F. Troncoso ◽  
Gabriel A. Rabinovich ◽  
Karina V. Mariño ◽  
María T. Elola
Keyword(s):  
Tandem Repeat ◽  
Cell Function ◽  
Full Length ◽  
Carbohydrate Recognition ◽  
Linker Peptide ◽  
Carbohydrate Recognition Domains ◽  
Function Relationship ◽  
Relationship Of ◽  
Group Structures

Galectin-8 (Gal-8) is a tandem-repeat type galectin with affinity for β-galactosides, bearing two carbohydrate recognition domains (CRD) connected by a linker peptide. The N- and C-terminal domains (Gal-8N and Gal-8C) share 35% homology, and their glycan ligand specificity is notably dissimilar: while Gal-8N shows strong affinity for α(2-3)-sialylated oligosaccharides, Gal-8C has higher affinity for non-sialylated oligosaccharides, including poly-N-acetyllactosamine and/ or A and B blood group structures. Particularly relevant for understanding the biological role of this lectin, full-length Gal-8 can bind cell surface glycoconjugates with broader affinity than the isolated Gal-8N and Gal-8C domains, a trait also described for other tandem-repeat galectins. Herein, we aim to discuss the potential use of separate CRDs in modelling tandem-repeat galectin-8 and its biological functions. For this purpose, we will cover several aspects of the structure–function relationship of this protein including crystallographic structures, glycan specificity, cell function and biological roles, with the ultimate goal of understanding the potential role of each CRD in predicting full-length Gal-8 involvement in relevant biological processes.

scholarly journals Structure-function relationship of a citrus salicylate methylesterase and role of salicylic acid in citrus canker resistance

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Caio Cesar de Lima Silva ◽  
Hugo Massayoshi Shimo ◽  
Rafael de Felício ◽  
Gustavo Fernando Mercaldi ◽  
Silvana Aparecida Rocco ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Structure Function ◽  
Citrus Canker ◽  
Structure Function Relationship ◽  
Function Relationship ◽  
Relationship Of

scholarly journals Computational Study on Temperature Driven Structure–Function Relationship of Polysaccharide Producing Bacterial Glycosyl Transferase Enzyme

Polymers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1771
Author(s):  
Patricio González-Faune ◽  
Ignacio Sánchez-Arévalo ◽  
Shrabana Sarkar ◽  
Krishnendu Majhi ◽  
Rajib Bandopadhyay ◽  
...  
Keyword(s):  
Structural Integrity ◽  
Computational Study ◽  
In Silico Analysis ◽  
Temperature Dependent ◽  
Bacterial Exopolysaccharide ◽  
Function Relationship ◽  
Industrial Level ◽  
Relationship Of ◽  
Bacterial Sources ◽  
Silico Analysis

Glycosyltransferase (GTs) is a wide class of enzymes that transfer sugar moiety, playing a key role in the synthesis of bacterial exopolysaccharide (EPS) biopolymer. In recent years, increased demand for bacterial EPSs has been observed in pharmaceutical, food, and other industries. The application of the EPSs largely depends upon their thermal stability, as any industrial application is mainly reliant on slow thermal degradation. Keeping this in context, EPS producing GT enzymes from three different bacterial sources based on growth temperature (mesophile, thermophile, and hyperthermophile) are considered for in silico analysis of the structural–functional relationship. From the present study, it was observed that the structural integrity of GT increases significantly from mesophile to thermophile to hyperthermophile. In contrast, the structural plasticity runs in an opposite direction towards mesophile. This interesting temperature-dependent structural property has directed the GT–UDP-glucose interactions in a way that thermophile has finally demonstrated better binding affinity (−5.57 to −10.70) with an increased number of hydrogen bonds (355) and stabilizing amino acids (Phe, Ala, Glu, Tyr, and Ser). The results from this study may direct utilization of thermophile-origin GT as best for industrial-level bacterial polysaccharide production.

scholarly journals Microsecond simulation unravel the structural dynamics of SARS-CoV-2 Spike-C-terminal cytoplasmic tail (residues 1242-1273)

2021 ◽  
Author(s):  
Prateek Kumar ◽  
Taniya Bhardwaj ◽  
Neha Garg ◽  
Rajanish Giri
Keyword(s):  
Structural Dynamics ◽  
Viral Proteins ◽  
Spike Protein ◽  
Temperature Dependent ◽  
Replica Exchange Molecular Dynamics ◽  
Structural Conformation ◽  
Human Coronaviruses ◽  
Function Relationship ◽  
Dynamics Simulations ◽  
Relationship Of

AbstractSpike protein of human coronaviruses has been a vital drug and vaccine target. The multifunctionality of this protein including host receptor binding and apoptosis has been proved in several coronaviruses. It also interacts with other viral proteins such as membrane (M) protein through its C-terminal domain. The specific dibasic motif signal present in cytosolic region at C-terminal of spike protein helps it to localize within the endoplasmic reticulum (ER). However, the structural conformation of cytosolic region is not known in SARS-CoV-2 using which it interacts with other proteins and transporting vesicles. Therefore, we have demonstrated the conformation of cytosolic region and its dynamics through computer simulations up to microsecond timescale using OPLS and CHARMM forcefields. The simulations have revealed the unstructured conformation of cytosolic region (residues 1242-1273). Also, in temperature dependent replica-exchange molecular dynamics simulations it has shown to form secondary structures. We believe that our findings will surely help us understand the structure-function relationship of the spike protein’s cytosolic region.

scholarly journals Role of membrane-associated thiol groups in the functional regulation of gastric microsomal (H+ + K+)-transporting ATPase system

1983 ◽  
Vol 213 (3) ◽  
pp. 587-594 ◽  
Author(s):  
J Nandi ◽  
Z Meng-Ai ◽  
T K Ray
Keyword(s):  
Structure Function ◽  
Thiol Groups ◽  
Dye Uptake ◽  
Atpase System ◽  
Structure Function Relationship ◽  
Functional Regulation ◽  
Function Relationship ◽  
Relationship Of ◽  
Stimulation Of

The distribution of free thiol groups associated with the membrane proteins of the purified pig gastric microsomal vesicles was quantified, and the relation of thiol groups to the function of the gastric (H+ + K+)-transporting ATPase system was investigated. Two different thiol-specific agents, carboxypyridine disulphide (CPDS) and N-(1-naphthyl)maleimide (NNM) were used for the study. The structure-function relationship of the membrane thiol groups was studied after modification by the probes under various conditions, relating the inhibition of the (H+ + K+)-transporting ATPase to the ATP-dependent H+ accumulation by the gastric microsomal vesicles. On the basis of the extent of stimulation of the microsomal (H+ + K+)-transporting ATPase in the presence and absence of valinomycin (val) about 85% of the vesicles were found to be intact. CPDS at 1 mM completely inhibits the valinomycin-stimulated ATPase and the associated p-nitrophenyl phosphatase with a concomitant inhibition of vesicular H+ uptake. Both the enzyme and dye-uptake activities were fully protected against CPDS inhibition when the treatment with CPDS was carried out in the presence of ATP. ATP also offered protection (about 65%) against NNM inhibition of the (H+ + K+)-transporting ATPase system and vesicular H+ uptake. Under similar conditions ATP also protected about 10 and 6 nmol of thiol groups/mg of protein respectively from CPDS and NNM reaction. Our data suggest that the thiol groups on the outer surface of the vesicles are primarily involved in gastric (H+ + K+)-transporting ATPase function. Furthermore, at least about 15% of the total microsomal thiol groups appear to be associated with the ATPase system. The data have been discussed in terms of the structure-function relationship of gastric microsomes.

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