scholarly journals Module organizational principles and dynamics in biological networks

2014 ◽  
Author(s):  
Chun-Yu Lin ◽  
Tsai-ling Lee ◽  
Yi-Wei Lin ◽  
Yu-Shu Lo ◽  
Chih-Ta Lin ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Biological Networks ◽  
Biological Functions ◽  
Time And Space ◽  
Interface Evolution ◽  
The Core ◽  
Core Proteins ◽  
Core Components ◽  
Highly Correlated ◽  
Organizational Principles

AbstractA module is a group of closely related proteins that act in concert to perform specific biological functions through protein–protein interactions (PPIs) that occur in time and space. However, the underlying organizational principles of a module remain unclear. In this study, we collected CORUM module templates to infer respective module families, including 58,041 homologous modules in 1,678 species, and PPI families using searches of complete genomic database. We then derived PPI evolution scores (PPIES) and interface evolution scores (IES) to infer module elements, including core and ring components. Functions of core components were highly correlated (Pearson’s r = 0.98) with those of 11,384 essential genes. In comparison with ring components, core proteins and PPIs were conserved in multiple species. Subsequently, protein dynamics and module dynamics of biological networks and functional diversities confirmed that core components form dynamic biological network hubs and play key roles in various biological functions. PPIES and IES can reflect module organization principles and protein/module dynamics in biological networks. On the basis of the analyses of gene essentiality, module dynamics, network topology, and gene co-expression, the module organizational principles can be described as follows: 1) a module consists of core and ring components; 2) the core components play major roles in biological functions and collaborate with ring components to perform certain functions in some cases; 3) the core components are conserved and essential in module dynamics in time and space.

scholarly journals Chondroitin Sulfate/Dermatan Sulfate-Protein Interactions and Their Biological Functions in Human Diseases: Implications and Analytical Tools

2021 ◽  
Vol 9 ◽  
Author(s):  
Bin Zhang ◽  
Lianli Chi
Keyword(s):  
Cell Surface ◽  
Chondroitin Sulfate ◽  
Protein Interactions ◽  
Dermatan Sulfate ◽  
Interaction Analysis ◽  
Structural Complexity ◽  
Protein Characterization ◽  
Biological Functions ◽  
Gag Protein ◽  
Core Proteins

Chondroitin sulfate (CS) and dermatan sulfate (DS) are linear anionic polysaccharides that are widely present on the cell surface and in the cell matrix and connective tissue. CS and DS chains are usually attached to core proteins and are present in the form of proteoglycans (PGs). They not only are important structural substances but also bind to a variety of cytokines, growth factors, cell surface receptors, adhesion molecules, enzymes and fibrillary glycoproteins to execute series of important biological functions. CS and DS exhibit variable sulfation patterns and different sequence arrangements, and their molecular weights also vary within a large range, increasing the structural complexity and diversity of CS/DS. The structure-function relationship of CS/DS PGs directly and indirectly involves them in a variety of physiological and pathological processes. Accumulating evidence suggests that CS/DS serves as an important cofactor for many cell behaviors. Understanding the molecular basis of these interactions helps to elucidate the occurrence and development of various diseases and the development of new therapeutic approaches. The present article reviews the physiological and pathological processes in which CS and DS participate through their interactions with different proteins. Moreover, classic and emerging glycosaminoglycan (GAG)-protein interaction analysis tools and their applications in CS/DS-protein characterization are also discussed.

scholarly journals Assisted assembly of bacteriophage T7 core components for genome translocation across the bacterial envelope

2021 ◽  
Vol 118 (34) ◽  
pp. e2026719118
Author(s):  
Mar Pérez-Ruiz ◽  
Mar Pulido-Cid ◽  
Juan Román Luque-Ortega ◽  
José María Valpuesta ◽  
Ana Cuervo ◽  
...  
Keyword(s):  
Bacteriophage T7 ◽  
Dna Translocation ◽  
Oligomeric State ◽  
Viral Dna ◽  
The Core ◽  
Cryo Electron Microscopy ◽  
Core Proteins ◽  
Core Components ◽  
Bacterial Cytoplasm ◽  
Bacterial Peptidoglycan

In most bacteriophages, genome transport across bacterial envelopes is carried out by the tail machinery. In viruses of the Podoviridae family, in which the tail is not long enough to traverse the bacterial wall, it has been postulated that viral core proteins assembled inside the viral head are translocated and reassembled into a tube within the periplasm that extends the tail channel. Bacteriophage T7 infects Escherichia coli, and despite extensive studies, the precise mechanism by which its genome is translocated remains unknown. Using cryo-electron microscopy, we have resolved the structure of two different assemblies of the T7 DNA translocation complex composed of the core proteins gp15 and gp16. Gp15 alone forms a partially folded hexamer, which is further assembled upon interaction with gp16 into a tubular structure, forming a channel that could allow DNA passage. The structure of the gp15–gp16 complex also shows the location within gp16 of a canonical transglycosylase motif involved in the degradation of the bacterial peptidoglycan layer. This complex docks well in the tail extension structure found in the periplasm of T7-infected bacteria and matches the sixfold symmetry of the phage tail. In such cases, gp15 and gp16 that are initially present in the T7 capsid eightfold-symmetric core would change their oligomeric state upon reassembly in the periplasm. Altogether, these results allow us to propose a model for the assembly of the core translocation complex in the periplasm, which furthers understanding of the molecular mechanism involved in the release of T7 viral DNA into the bacterial cytoplasm.

Protein–protein interactions in the archaeal core replisome

2011 ◽  
Vol 39 (1) ◽  
pp. 163-168 ◽  
Author(s):  
Stuart A. MacNeill
Keyword(s):  
Protein Interactions ◽  
Current Knowledge ◽  
Sequence Similarity ◽  
Chromosome Replication ◽  
Model System ◽  
Protein Protein Interactions ◽  
Chromosomal Dna ◽  
The Core ◽  
Core Components ◽  
Replication Factors

Most of the core components of the archaeal chromosomal DNA replication apparatus share significant protein sequence similarity with eukaryotic replication factors, making the Archaea an excellent model system for understanding the biology of chromosome replication in eukaryotes. The present review summarizes current knowledge of how the core components of the archaeal chromosome replication apparatus interact with one another to perform their essential functions.

scholarly journals CORO7 functions as a scaffold protein for the core kinase complex assembly of the Hippo pathway

2020 ◽  
pp. jbc.RA120.013297
Author(s):  
Jina Park ◽  
Kyoungho Jun ◽  
Yujin Choi ◽  
Eunju Yoon ◽  
Wonho Kim ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Mammalian Cells ◽  
Molecular Mechanisms ◽  
Hippo Pathway ◽  
Cell Contact ◽  
Protein Protein Interactions ◽  
The Core ◽  
Core Components ◽  
Pathway Regulation ◽  
The Hippo Pathway

The Hippo pathway controls organ size and tissue homeostasis through the regulation of cell proliferation and apoptosis. However, the exact molecular mechanisms underpinning Hippo pathway regulation is not fully understood. Here, we identify a new component of the Hippo pathway: CORO7, a coronin protein family member that is involved in organization of the actin cytoskeleton. pod1, the Drosophila orthologue of CORO7, genetically interacts with key Hippo pathway genes in Drosophila. In mammalian cells, CORO7 is required for the activation of the Hippo pathway in response to cell-cell contact, serum deprivation, and cytoskeleton damage. CORO7 forms a complex with the core components of the pathway and functions as a scaffold for the Hippo core kinase complex. Collectively, these results demonstrate that CORO7 is a key scaffold controlling the Hippo pathway via modulating protein-protein interactions.

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 Hakai is required for stabilization of core components of the m6A mRNA methylation machinery

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Praveen Bawankar ◽  
Tina Lence ◽  
Chiara Paolantoni ◽  
Irmgard U. Haussmann ◽  
Migle Kazlauskiene ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Sex Determination ◽  
Ubiquitin Ligase ◽  
Mammalian Cells ◽  
E3 Ubiquitin Ligase ◽  
Human Cells ◽  
Biological Functions ◽  
Mrna Metabolism ◽  
Mrna Methylation ◽  
Core Components

AbstractN6-methyladenosine (m6A) is the most abundant internal modification on mRNA which influences most steps of mRNA metabolism and is involved in several biological functions. The E3 ubiquitin ligase Hakai was previously found in complex with components of the m6A methylation machinery in plants and mammalian cells but its precise function remained to be investigated. Here we show that Hakai is a conserved component of the methyltransferase complex in Drosophila and human cells. In Drosophila, its depletion results in reduced m6A levels and altered m6A-dependent functions including sex determination. We show that its ubiquitination domain is required for dimerization and interaction with other members of the m6A machinery, while its catalytic activity is dispensable. Finally, we demonstrate that the loss of Hakai destabilizes several subunits of the methyltransferase complex, resulting in impaired m6A deposition. Our work adds functional and molecular insights into the mechanism of the m6A mRNA writer complex.

scholarly journals The core components of education 4.0 in higher education: Three case studies in engineering education

2021 ◽  
Vol 93 ◽  
pp. 107278
Author(s):  
Jhonattan Miranda ◽  
Christelle Navarrete ◽  
Julieta Noguez ◽  
José-Martin Molina-Espinosa ◽  
María-Soledad Ramírez-Montoya ◽  
...  
Keyword(s):  
Higher Education ◽  
Engineering Education ◽  
Case Studies ◽  
The Core ◽  
Core Components
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