scholarly journals Polyamines Disrupt the KaiABC Oscillator by Inducing Protein Denaturation

Molecules ◽  
2019 ◽  
Vol 24 (18) ◽  
pp. 3351 ◽  
Author(s):  
Jinkui Li ◽  
Lingya Zhang ◽  
Junwen Xiong ◽  
Xiyao Cheng ◽  
Yongqi Huang ◽  
...  
Keyword(s):  
Protein Denaturation ◽  
Structure And Function ◽  
Clock Proteins ◽  
In Vitro Reconstitution ◽  
Living Organisms ◽  
And Function ◽  
Cellular Components ◽  
The Impact

Polyamines are positively charged small molecules ubiquitously existing in all living organisms, and they are considered as one kind of the most ancient cellular components. The most common polyamines are spermidine, spermine, and their precursor putrescine generated from ornithine. Polyamines play critical roles in cells by stabilizing chromatin structure, regulating DNA replication, modulating gene expression, etc., and they also affect the structure and function of proteins. A few studies have investigated the impact of polyamines on protein structure and function previously, but no reports have focused on a protein-based biological module with a dedicated function. In this report, we investigated the impact of polyamines (putrescine, spermidine, and spermine) on the cyanobacterial KaiABC circadian oscillator. Using an established in vitro reconstitution system, we noticed that polyamines could disrupt the robustness of the KaiABC oscillator by inducing the denaturation of the Kai proteins (KaiA, KaiB, and KaiC). Further experiments showed that the denaturation was likely due to the induced change of the thermal stability of the clock proteins. Our study revealed an intriguing role of polyamines as a component in complex cellular environments and would be of great importance for elucidating the biological function of polyamines in future.

scholarly journals Regulation of phagolysosomal activity by miR-204 critically influences structure and function of retinal pigment epithelium/retina

2019 ◽  
Vol 28 (20) ◽  
pp. 3355-3368 ◽  
Author(s):  
Congxiao Zhang ◽  
Kiyoharu J Miyagishima ◽  
Lijin Dong ◽  
Aaron Rising ◽  
Malika Nimmagadda ◽  
...  
Keyword(s):  
Retinal Pigment Epithelium ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Primary Cultures ◽  
Structure And Function ◽  
Apical Surface ◽  
Altered Expression ◽  
And Function ◽  
The Impact

Abstract MicroRNA-204 (miR-204) is expressed in pulmonary, renal, mammary and eye tissue, and its reduction can result in multiple diseases including cancer. We first generated miR-204−/− mice to study the impact of miR-204 loss on retinal and retinal pigment epithelium (RPE) structure and function. The RPE is fundamentally important for maintaining the health and integrity of the retinal photoreceptors. miR-204−/− eyes evidenced areas of hyper-autofluorescence and defective photoreceptor digestion, along with increased microglia migration to the RPE. Migratory Iba1+ microglial cells were localized to the RPE apical surface where they participated in the phagocytosis of photoreceptor outer segments (POSs) and contributed to a persistent build-up of rhodopsin. These structural, molecular and cellular outcomes were accompanied by decreased light-evoked electrical responses from the retina and RPE. In parallel experiments, we suppressed miR-204 expression in primary cultures of human RPE using anti-miR-204. In vitro suppression of miR-204 in human RPE similarly showed abnormal POS clearance and altered expression of autophagy-related proteins and Rab22a, a regulator of endosome maturation. Together, these in vitro and in vivo experiments suggest that the normally high levels of miR-204 in RPE can mitigate disease onset by preventing generation of oxidative stress and inflammation originating from intracellular accumulation of undigested photoreactive POS lipids. More generally, these results implicate RPE miR-204-mediated regulation of autophagy and endolysosomal interaction as a critical determinant of normal RPE/retina structure and function.

A stochastic roadmap method to model protein structural transitions

Robotica ◽  
2015 ◽  
Vol 34 (8) ◽  
pp. 1705-1733 ◽  
Author(s):  
Kevin Molloy ◽  
Rudy Clausen ◽  
Amarda Shehu
Keyword(s):  
Protein Structure ◽  
Molecular Basis ◽  
Structure And Function ◽  
Structural Transitions ◽  
Simulation Framework ◽  
Human Disorders ◽  
Model Protein ◽  
And Function ◽  
The Impact

SUMMARYEvidence is emerging that the role of protein structure in disease needs to be rethought. Sequence mutations in proteins are often found to affect the rate at which a protein switches between structures. Modeling structural transitions in wildtype and variant proteins is central to understanding the molecular basis of disease. This paper investigates an efficient algorithmic realization of the stochastic roadmap simulation framework to model structural transitions in wildtype and variants of proteins implicated in human disorders. Our results indicate that the algorithm is able to extract useful information on the impact of mutations on protein structure and function.

scholarly journals The conformational and mutational landscape of the ubiquitin-like marker for the autophagosome formation in cancer

2019 ◽  
Author(s):  
Burcu Aykac Fas ◽  
Mukesh Kumar ◽  
Valentina Sora ◽  
Maliha Mashkoor ◽  
Matteo Lambrughi ◽  
...  
Keyword(s):  
Physical Models ◽  
Missense Mutations ◽  
Cancer Types ◽  
Neutral Mutations ◽  
And Function ◽  
Cellular Components ◽  
The Impact ◽  
Pan Cancer ◽  
Structural Ensemble

AbstractAutophagy is a cellular process to recycle damaged cellular components and its modulation can be exploited for disease treatments. A key autophagy player is a ubiquitin-like protein, LC3B. Compelling evidence attests the role of autophagy and LC3B in different cancer types. Many LC3B structures have been solved, but a comprehensive study, including dynamics, has not been yet undertaken. To address this knowledge gap, we assessed ten physical models for molecular dynamics for their capabilities to describe the structural ensemble of LC3B in solution using different metrics and comparison with NMR data. With the resulting LC3B ensembles, we characterized the impact of 26 missense mutations from Pan-Cancer studies with different approaches. Our findings shed light on driver or neutral mutations in LC3B, providing an atlas of its modifications in cancer. Our framework could be used to assess the pathogenicity of mutations by accounting for the different aspects of protein structure and function altered by mutational events.

scholarly journals CNBP controls transcription by unfolding DNA G-quadruplex structures

2019 ◽  
Vol 47 (15) ◽  
pp. 7901-7913 ◽  
Author(s):  
Aldana P David ◽  
Angélique Pipier ◽  
Federico Pascutti ◽  
Andrés Binolfi ◽  
Andrea M J Weiner ◽  
...  
Keyword(s):  
Transcriptional Control ◽  
Regulatory Elements ◽  
Transcription Start Sites ◽  
G4 Dna ◽  
Dna Strands ◽  
Living Organisms ◽  
And Function

Abstract Guanine-rich DNA strands can fold into non-canonical four-stranded secondary structures named G-quadruplexes (G4). Experimental evidences suggest that G4-DNA surrounding transcription start sites act as cis-regulatory elements by either stimulating or inhibiting gene transcription. Therefore, proteins able to target and regulate specific G4 formation/unfolding are crucial for G4-mediated transcriptional control. Here we present data revealing that CNBP acts in vitro as a G4-unfolding protein over a tetramolecular G4 formed by the TG4T oligonucleotide, as well as over the G4 folded in the promoters of several oncogenes. CNBP depletion in cellulo led to a reduction in the transcription of endogenous KRAS, suggesting a regulatory role of CNBP in relieving the transcriptional abrogation due to G4 formation. CNBP activity was also assayed over the evolutionary conserved G4 enhancing the transcription of NOGGIN (NOG) developmental gene. CNBP unfolded in vitro NOG G4 and experiments performed in cellulo and in vivo in developing zebrafish showed a repressive role of CNBP on the transcription of this gene by G4 unwinding. Our results shed light on the mechanisms underlying CNBP way of action, as well as reinforce the notion about the existence and function of G4s in whole living organisms.

scholarly journals Morphofunctional platform for forming clinical symptoms of celiakia in children with connective tissue dysplasia

2021 ◽  
pp. 129-135
Author(s):  
Z. V. Nesterenko
Keyword(s):  
Celiac Disease ◽  
Connective Tissue ◽  
Clinical Manifestations ◽  
Structure And Function ◽  
Connective Tissue Disorders ◽  
Diverse Range ◽  
Organ Systems ◽  
And Function ◽  
The Impact

Review article on the problem of celiac disease, which is widespread with diverse range of clinical manifestations and inadequate diagnosis, is presented. The conciderable prevalence of connective tissue disorders in the pediatric population, the important role of connective tissue in the function of all organ systems, including the gastrointestinal system, necessitates studying the impact of the impaired structure and function of connective tissue on the development of celiac symptoms. The paper describes the historical development of the concept of “celiac disease”, the process of studying the pattern of the onset and development of symptoms of the disease; modern studies explaining the varied complex mechanisms of the disease.The article cites the researchers who studied the role of connective tissue in the structure and function of all body systems with identifying the impact of connective tissue disorders on the development of the gastrointestinal pathology (abnormal motor- tonic activity, reflux disease, dysbiosis, disturbance of autonomic homeostasis) and the manifestation of celiac disease associated with connective tissue disorders.The conclusion stresses the need to consider the problem of celiac disease as a manifestation of the pathology of the whole organism with the obligatory diagnosis of comorbid diseases, including those associated with connective tissue disorders, which will provide a more successful therapy for celiac disease and an improved prognosis.

scholarly journals Structure and function of small airways in asthma patients revisited

2021 ◽  
Vol 30 (159) ◽  
pp. 200186
Author(s):  
Wytse B. van den Bosch ◽  
Alan L. James ◽  
Harm A.W.M. Tiddens
Keyword(s):  
Extracellular Matrix ◽  
Asthma Severity ◽  
Structure And Function ◽  
Small Airways ◽  
Asthma Patients ◽  
Almost All ◽  
And Function ◽  
Modelling Methods

Small airways (<2 mm in diameter) are probably involved across almost all asthma severities and they show proportionally more structural and functional abnormalities with increasing asthma severity. The structural and functional alterations of the epithelium, extracellular matrix and airway smooth muscle in small airways of people with asthma have been described over many years using in vitro studies, animal models or imaging and modelling methods. The purpose of this review was to provide an overview of these observations and to outline several potential pathophysiological mechanisms regarding the role of small airways in asthma.

scholarly journals Fine Carbohydrate Structure of Dietary Resistant Glucans Governs the Structure and Function of Human Gut Microbiota

Nutrients ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 2924
Author(s):  
Arianna D. Romero Marcia ◽  
Tianming Yao ◽  
Ming-Hsu Chen ◽  
Renee E. Oles ◽  
Stephen R. Lindemann
Keyword(s):  
Community Structure ◽  
Structure And Function ◽  
Growth Responses ◽  
Sugar Composition ◽  
Functional Responses ◽  
Human Gut ◽  
Fatty Acid Production ◽  
And Function ◽  
The Impact

Increased dietary fiber consumption has been shown to increase human gut microbial diversity, but the mechanisms driving this effect remain unclear. One possible explanation is that microbes are able to divide metabolic labor in consumption of complex carbohydrates, which are composed of diverse glycosidic linkages that require specific cognate enzymes for degradation. However, as naturally derived fibers vary in both sugar composition and linkage structure, it is challenging to separate out the impact of each of these variables. We hypothesized that fine differences in carbohydrate linkage structure would govern microbial community structure and function independently of variation in glycosyl residue composition. To test this hypothesis, we fermented commercially available soluble resistant glucans, which are uniformly composed of glucose linked in different structural arrangements, in vitro with fecal inocula from each of three individuals. We measured metabolic outputs (pH, gas, and short-chain fatty acid production) and community structure via 16S rRNA amplicon sequencing. We determined that community metabolic outputs from identical glucans were highly individual, emerging from divergent initial microbiome structures. However, specific operational taxonomic units (OTUs) responded similarly in growth responses across individuals’ microbiota, though in context-dependent ways; these data suggested that certain taxa were more efficient in competing for some structures than others. Together, these data support the hypothesis that variation in linkage structure, independent of sugar composition, governs compositional and functional responses of microbiota.

scholarly journals Modulation of autophagy by RTN-1C: role in autophagosome biogenesis

2019 ◽  
Vol 10 (12) ◽  
Author(s):  
Manuela D’ Eletto ◽  
Anna Risuglia ◽  
Serafina Oliverio ◽  
Bisan Mehdawy ◽  
Roberta Nardacci ◽  
...  
Keyword(s):  
Stress Condition ◽  
Structure And Function ◽  
Autophagy Induction ◽  
Vesicle Biogenesis ◽  
Experimental Approaches ◽  
Apoptotic Pathways ◽  
And Function ◽  
The Impact ◽  
Er Membrane

AbstractThe endoplasmic reticulum (ER) is a key organelle fundamental for the maintenance of cellular homeostasis and to determine the cell’s fate under stress conditions. Among the known proteins that regulate ER structure and function there is Reticulon-1C (RTN-1C), a member of the reticulon family localized primarily on the ER membrane. We previously demonstrated that RTN-1C expression affects ER function and stress condition. ER is an essential site for the regulation of apoptotic pathways and it has also been recently recognized as an important component of autophagic signaling. Based on these evidences, we have investigated the impact of RTN-1C modulation on autophagy induction. Interestingly we found that reticulon overexpression is able to activate autophagic machinery and its silencing results in a significative inhibition of both basal and induced autophagic response. Using different experimental approaches we demonstrated that RTN-1C colocalizes with ATG16L and LC3II on the autophagosomes. Considering the key role of reticulon proteins in the control of ER membrane shaping and homeostasis, our data suggest the participation of RTN-1C in the autophagic vesicle biogenesis at the level of the ER compartment. Our data indicate a new mechanism by which this structural ER protein modulates cellular stress, that is at the basis of different autophagy-related pathologies.

scholarly journals The cloning revolution: DNA cloning and biochemistry

2007 ◽  
Vol 29 (5) ◽  
pp. 12-15
Author(s):  
James L. Hartley
Keyword(s):  
Information Retrieval ◽  
World Wide ◽  
Structure And Function ◽  
Chemical Processes ◽  
Reference Source ◽  
Dna Cloning ◽  
The World ◽  
Living Organisms ◽  
And Function ◽  
Cellular Components

According to the online reference source Wikipedia (www.wikipedia.org), biochemistry is “the study of the chemical processes and transformations in living organisms. It deals with the structure and function of cellular components, such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules.” It seems appropriate to start with a definition from the World Wide Web, which has changed information retrieval as much as DNA cloning has changed biochemistry. Here I attempt to provide some perspectives on that transformation.

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