scholarly journals Elucidating Carbohydrate-Protein Interactions Using Nanoparticle-Based Approaches

2021 ◽  
Vol 9 ◽  
Author(s):  
Dongyoon Kim ◽  
Nowras Rahhal ◽  
Christoph Rademacher
Keyword(s):  
Protein Interactions ◽  
Early Recognition ◽  
Particle Surface ◽  
Biological Response ◽  
Cellular Interactions ◽  
Molecular Fingerprints ◽  
Cellular Immunology ◽  
Promising Tool ◽  
Cellular Context ◽  
Molecular Patterns

Carbohydrates are present on every living cell and coordinate important processes such as self/non-self discrimination. They are amongst the first molecular determinants to be encountered when cellular interactions are initiated. In particular, they resemble essential molecular fingerprints such as pathogen-, danger-, and self-associated molecular patterns guiding key decision-making in cellular immunology. Therefore, a deeper understanding of how cellular receptors of the immune system recognize incoming particles, based on their carbohydrate signature and how this information is translated into a biological response, will enable us to surgically manipulate them and holds promise for novel therapies. One approach to elucidate these early recognition events of carbohydrate interactions at cellular surfaces is the use of nanoparticles coated with defined carbohydrate structures. These particles are captured by carbohydrate receptors and initiate a cellular cytokine response. In the case of endocytic receptors, the capturing enables the engulfment of exogenous particles. Thereafter, the particles are sorted and degraded during their passage in the endolysosomal pathway. Overall, these processes are dependent on the nature of the endocytic carbohydrate receptors and consequently reflect upon the carbohydrate patterns on the exogenous particle surface. This interplay is still an under-studied subject. In this review, we summarize the application of nanoparticles as a promising tool to monitor complex carbohydrate-protein interactions in a cellular context and their application in areas of biomedicine.

Algorithmic and Stochastic Representations of Gene Regulatory Networks and Protein-Protein Interactions

2019 ◽  
Vol 19 (6) ◽  
pp. 413-425 ◽  
Author(s):  
Athanasios Alexiou ◽  
Stylianos Chatzichronis ◽  
Asma Perveen ◽  
Abdul Hafeez ◽  
Ghulam Md. Ashraf
Keyword(s):  
Protein Interactions ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Review Paper ◽  
Boolean Networks ◽  
Diagnostic Tools ◽  
Complex Nature ◽  
Cellular Interactions ◽  
Protein Protein Interactions ◽  
Deterministic Models

Background:Latest studies reveal the importance of Protein-Protein interactions on physiologic functions and biological structures. Several stochastic and algorithmic methods have been published until now, for the modeling of the complex nature of the biological systems.Objective:Biological Networks computational modeling is still a challenging task. The formulation of the complex cellular interactions is a research field of great interest. In this review paper, several computational methods for the modeling of GRN and PPI are presented analytically.Methods:Several well-known GRN and PPI models are presented and discussed in this review study such as: Graphs representation, Boolean Networks, Generalized Logical Networks, Bayesian Networks, Relevance Networks, Graphical Gaussian models, Weight Matrices, Reverse Engineering Approach, Evolutionary Algorithms, Forward Modeling Approach, Deterministic models, Static models, Hybrid models, Stochastic models, Petri Nets, BioAmbients calculus and Differential Equations.Results:GRN and PPI methods have been already applied in various clinical processes with potential positive results, establishing promising diagnostic tools.Conclusion:In literature many stochastic algorithms are focused in the simulation, analysis and visualization of the various biological networks and their dynamics interactions, which are referred and described in depth in this review paper.

scholarly journals Distinct carbohydrate and lipid-based molecular patterns within lipopolysaccharides from Burkholderia cepacia contribute to defense-associated differential gene expression in Arabidopsis thaliana

2011 ◽  
Vol 18 (1) ◽  
pp. 140-154 ◽  
Author(s):  
Ntakadzeni E Madala ◽  
Antonio Molinaro ◽  
Ian A Dubery
Keyword(s):  
Arabidopsis Thaliana ◽  
Protein Interactions ◽  
Stress Responses ◽  
Burkholderia Cepacia ◽  
Lipid A ◽  
Metabolic Reprogramming ◽  
Basal Resistance ◽  
Signal Perception ◽  
Initial Perception ◽  
Molecular Patterns

Lipopolysaccharides are structural components within the cell walls of Gram-negative bacteria. The LPSs as microbe-associated molecular pattern (MAMP) molecules can trigger defense-related responses involved in MAMP-triggered immunity and basal resistance in plants, presumably from an initial perception event. LPS from Burkholderia cepacia as well as two fragments, the glycolipid, lipid A and the polysaccharide (OPS-core) chain, were used to treat Arabidopsis thaliana seedlings to evaluate the eliciting activities of the individual LPS sub-domains by means of Annealing Control Primer-based Differential Display transcript profiling. Genes found to be up-regulated encode for proteins involved in signal perception and transduction, transcriptional regulation and defense – and stress responses. Furthermore, genes encoding proteins involved in chaperoning, secretion, protein–protein interactions and protein degradation were differentially expressed. It is concluded that intact LPS, as well as the two sub-components, induced the expression of a broad range of genes associated with perception and defense as well as metabolic reprogramming of cellular activities in support of immunity and basal resistance. Whilst the lipid A and OPS moieties were able to up-regulate sub-sets of defense-associated genes over the same spectrum of categories as intact LPS, the up-regulation observed with intact LPS was the more comprehensive, suggesting that the lipid A and glycan molecular patterns of the molecule act as partial agonists, but that the intact LPS structure is required for full agonist activity.

scholarly journals Insights into the Periplasmic Proteins of Acinetobacter baumannii AB5075 and the Impact of Imipenem Exposure: A Proteomic Approach

2019 ◽  
Vol 20 (14) ◽  
pp. 3451 ◽  
Author(s):  
Scribano ◽  
Marzano ◽  
Mortera ◽  
Sarshar ◽  
Vernocchi ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Antibiotic Resistance ◽  
Acinetobacter Baumannii ◽  
Protein Interactions ◽  
Biological Response ◽  
Bacterial Viability ◽  
Proteomic Approach ◽  
Periplasmic Proteins ◽  
General Response ◽  
The Impact

Carbapenem-resistant Acinetobacter baumannii strains cause life-threatening infections due to the lack of therapeutic options. Although the main mechanisms underlying antibiotic-resistance have been extensively studied, the general response to maintain bacterial viability under antibiotic exposure deserves to be fully investigated. Since the periplasmic space contains several proteins with crucial cellular functions, besides carbapenemases, we decided to study the periplasmic proteome of the multidrug-resistant (MDR) A. baumannii AB5075 strain, grown in the absence and presence of imipenem (IMP). Through the proteomic approach, 65 unique periplasmic proteins common in both growth conditions were identified: eight proteins involved in protein fate, response to oxidative stress, energy metabolism, antibiotic-resistance, were differentially expressed. Among them, ABUW_1746 and ABUW_2363 gene products presented the tetratricopeptide repeat motif, mediating protein-protein interactions. The expression switch of these proteins might determine specific protein interactions to better adapt to changing environmental conditions. ABUW_2868, encoding a heat shock protein likely involved in protection against oxidative stress, was upregulated in IMP-exposed bacteria. Accordingly, the addition of periplasmic proteins from A. baumannii cultured with IMP increased bacterial viability in an antioxidant activity assay. Overall, this study provides the first insights about the composition of the periplasmic proteins of a MDR A. baumannii strain, its biological response to IMP and suggests possible new targets to develop alternative antibiotic drugs.

scholarly journals Osteoblasts Growth Behaviour on Bio-Based Calcium Carbonate Aragonite Nanocrystal

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Abdullahi Shafiu Kamba ◽  
Zuki Abu Bakar Zakaria
Keyword(s):  
Calcium Carbonate ◽  
Fluorescent Microscopy ◽  
Membrane Integrity ◽  
Biological Response ◽  
Cellular Interactions ◽  
Cell Membrane Integrity ◽  
Native Bone ◽  
Composition Structure ◽  
Stimulate Osteoblast Differentiation

Calcium carbonate (CaCO3) nanocrystals derived from cockle shells emerge to present a good concert in bone tissue engineering because of their potential to mimic the composition, structure, and properties of native bone. The aim of this study was to evaluate the biological response of CaCO3nanocrystals on hFOB 1.19 and MC3T3 E-1 osteoblast cellsin vitro. Cell viability and proliferation were assessed by MTT and BrdU assays, and LDH was measured to determine the effect of CaCO3nanocrystals on cell membrane integrity. Cellular morphology was examined by SEM and fluorescence microscopy. The results showed that CaCO3nanocrystals had no toxic effects to some extent. Cell proliferation, alkaline phosphatase activity, and protein synthesis were enhanced by the nanocrystals when compared to the control. Cellular interactions were improved, as indicated by SEM and fluorescent microscopy. The production of VEGF and TGF-1 was also affected by the CaCO3nanocrystals. Therefore, bio-based CaCO3nanocrystals were shown to stimulate osteoblast differentiation and improve the osteointegration process.

scholarly journals A B23-interacting sequence as a tool to visualize protein interactions in a cellular context

2007 ◽  
Vol 120 (2) ◽  
pp. 265-275 ◽  
Author(s):  
T. Lechertier ◽  
V. Sirri ◽  
D. Hernandez-Verdun ◽  
P. Roussel
Keyword(s):  
Protein Interactions ◽  
Cellular Context

scholarly journals CRISPR-Assisted Detection of RNA-Protein Interactions in Living Cells

2020 ◽  
Author(s):  
Wenkai Yi ◽  
Jingyu Li ◽  
Xiaoxuan Zhu ◽  
Xi Wang ◽  
Ligang Fan ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Binding Proteins ◽  
Living Cells ◽  
Molecular Engineering ◽  
Interaction Detection ◽  
Rna Targeting ◽  
Cellular Context ◽  
Non Coding Rnas ◽  
Co Precipitation ◽  
Functional Mechanisms

Abstract Delineating the protein network associated with long non-coding RNAs (lncRNAs) is fundamental to understanding the functional mechanisms of lncRNAs. Current methods to identify lncRNA-binding proteins either rely on crosslinking-mediated complex co-precipitation or require extensive molecular engineering, leading to drawbacks such as loss of cellular context and low capture efficiency. Here we describe a CRISPR-Assisted RNA-Protein Interaction Detection method (CARPID), which leverages CRISPR/CasRx-based RNA targeting and proximity labeling, to rapidly capture binding proteins of specific lncRNAs in their native cellular context followed by LC-MS/MS identification. Applied to a variety of lncRNAs of different lengths and subcellular localizations, CARPID is proven to be a reliable and robust tool to discover the binding proteins of lncRNAs inside living cells.

mARVCF cellular localisation and binding to cadherins is influenced by the cellular context but not by alternative splicing

2001 ◽  
Vol 114 (21) ◽  
pp. 3873-3884 ◽  
Author(s):  
Zoe Waibler ◽  
Annette Schäfer ◽  
Anna Starzinski-Powitz
Keyword(s):  
Alternative Splicing ◽  
Protein Interactions ◽  
Coiled Coil ◽  
Distinct Pattern ◽  
Subcellular Localisation ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
C Terminus ◽  
Coiled Coil Region ◽  
Cellular Context

ARVCF, a member of the catenin family, is thought to contribute to the morphoregulatory function of the cadherin-catenin complex. Recently, we reported the isolation and characterisation of murine ARVCF (mARVCF), particularly its interaction with M-cadherin. Here, we describe the identification of novel mARVCF isoforms that arise by alternative splicing. At the N-terminus, alternative splicing results in the inclusion or omission of a coiled-coil region probably important for protein-protein interactions. At the C-terminus, four isoforms also differ by domains potentially important for selective protein-protein interaction. The eight putative mARVCF isoforms were expressed as EGFP-fusion proteins in six different cell lines that exhibit a distinct pattern of cadherins. Apparently, binding of the mARVCF isoforms to M-, N-, or E-cadherin is generally unaffected by their altered N- and C-termini, as revealed by the MOM recruitment assay. However, mARVCF isoforms reproducibly exhibit differential localisation in distinct cellular environments. For example, mARVCF isoforms are unable to colocalise with N-cadherin in EJ28 carcinoma cells but do so in HeLa cells. Our results suggest that the subcellular localisation of mARVCF may be determined not only by the presence or absence of an appropriate interaction partner, in this case cadherins, but also by the cellular context.

scholarly journals The Structure of Human Parechovirus 1 Reveals an Association of the RNA Genome with the Capsid

2015 ◽  
Vol 90 (3) ◽  
pp. 1377-1386 ◽  
Author(s):  
Sergei Kalynych ◽  
Lenka Pálková ◽  
Pavel Plevka
Keyword(s):  
Small Molecules ◽  
Capsid Protein ◽  
Protein Interactions ◽  
Rna Binding ◽  
Particle Surface ◽  
Gastrointestinal Disorders ◽  
Human Parechovirus ◽  
Antiviral Compounds ◽  
Rna Genome

ABSTRACTParechoviruses are human pathogens that cause diseases ranging from gastrointestinal disorders to encephalitis. Unlike those of most picornaviruses, parechovirus capsids are composed of only three subunits: VP0, VP1, and VP3. Here, we present the structure of a human parechovirus 1 (HPeV-1) virion determined to a resolution of 3.1 Å. We found that interactions among pentamers in the HPeV-1 capsid are mediated by the N termini of VP0s, which correspond to the capsid protein VP4 and the N-terminal part of the capsid protein VP2 of other picornaviruses. In order to facilitate delivery of the virus genome into the cytoplasm, the N termini of VP0s have to be released from contacts between pentamers and exposed at the particle surface, resulting in capsid disruption. A hydrophobic pocket, which can be targeted by capsid-binding antiviral compounds in many other picornaviruses, is not present in HPeV-1. However, we found that interactions between the HPeV-1 single-stranded RNA genome and subunits VP1 and VP3 in the virion impose a partial icosahedral ordering on the genome. The residues involved in RNA binding are conserved among all parechoviruses, suggesting a putative role of the genome in virion stability or assembly. Therefore, putative small molecules that could disrupt HPeV RNA-capsid protein interactions could be developed into antiviral inhibitors.IMPORTANCEHuman parechoviruses (HPeVs) are pathogens that cause diseases ranging from respiratory and gastrointestinal disorders to encephalitis. Recently, there have been outbreaks of HPeV infections in Western Europe and North America. We present the first atomic structure of parechovirus HPeV-1 determined by X-ray crystallography. The structure explains why HPeVs cannot be targeted by antiviral compounds that are effective against other picornaviruses. Furthermore, we found that the interactions of the HPeV-1 genome with the capsid resulted in a partial icosahedral ordering of the genome. The residues involved in RNA binding are conserved among all parechoviruses, suggesting an evolutionarily fixed role of the genome in virion assembly. Therefore, putative small molecules disrupting HPeV RNA-capsid protein interactions could be developed into antiviral inhibitors.

scholarly journals CBRPP: a new RNA-centric method to study RNA-protein interactions

2020 ◽  
Author(s):  
Yunfei Li ◽  
Shengde Liu ◽  
Lili Cao ◽  
Yujie Luo ◽  
Hongqiang Du ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
High Specificity ◽  
Cellular Mechanism ◽  
Cross Linking ◽  
Cell Dysfunction ◽  
Cellular Context ◽  
Enzyme Labels ◽  
Target Rna

AbstractRNA-protein interactions play essential roles in tuning gene expression at RNA level and modulating the function of proteins. Abnormal RNA-protein interactions lead to cell dysfunction and human diseases. Therefore, mapping networks of RNA-protein interactions is crucial for understanding cellular mechanism and pathogenesis of diseases. Different practical protein-centric methods for studying RNA-protein interactions has been reported, but few RNA-centric methods exist. Here, we developed CRISPR-based RNA proximity proteomics (CBRPP), a new RNA-centric method to identify proteins associated with the target RNA in native cellular context without cross-linking or RNA manipulation in vitro. CBRPP is based on a fusion of dCas13 and proximity-based labeling (PBL) enzyme. dCas13 can deliver PBL enzyme to the target RNA with high specificity, while PBL enzyme labels the surrounding proteins of the target RNA, which are then identified by mass spectrometry.

Sign in / Sign up

Export Citation Format

Share Document