Specificity And Stability In Topology Of Protein Networks Pdf

specificity and stability in topology of protein networks pdf

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Progress in uncovering the protein interaction networks of several species has led to questions of what underlying principles might govern their organization.

Protein structure is the three-dimensional arrangement of atoms in an amino acid -chain molecule. A single amino acid monomer may also be called a residue indicating a repeating unit of a polymer.

Defining specific protein interactions and spatially or temporally restricted local proteomes improves our understanding of all cellular processes, but obtaining such data is challenging, especially for rare proteins, cell types, or events. Recent technological improvements, namely two highly active biotin ligase variants TurboID and miniTurbo , allowed us to address two challenging questions in plants: 1 what are in vivo partners of a low abundant key developmental transcription factor and 2 what is the nuclear proteome of a rare cell type? Proteins identified with FAMA-TurboID include known interactors of this stomatal transcription factor and novel proteins that could facilitate its activator and repressor functions. Directing TurboID to stomatal nuclei enabled purification of cell type- and subcellular compartment-specific proteins.

Specificity and Stability in Topology of Protein Networks

Thank you for visiting nature. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer. In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. The ability to predict protein—protein interactions is crucial to our understanding of a wide range of biological activities and functions in the human body, and for guiding drug discovery. Algebraic topology, a champion in recent worldwide competitions for protein—ligand binding affinity predictions, is a promising approach to simplifying the complexity of biological structures. Here we introduce element- and site-specific persistent homology a new branch of algebraic topology to simplify the structural complexity of protein—protein complexes and embed crucial biological information into topological invariants.

Thank you for visiting nature. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer. In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. Despite exceptional experimental efforts to map out the human interactome, the continued data incompleteness limits our ability to understand the molecular roots of human disease.

Either your web browser doesn't support Javascript or it is currently turned off. In the latter case, please turn on Javascript support in your web browser and reload this page. Author contributions: E. How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous nonfunctional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are directly determined from its genome through biophysical properties of protein structures and binding interactions in a crowded cellular environment. The model cell includes three independent prototypical pathways, whose topologies of protein—protein interaction PPI subnetworks are different, but whose contributions to the cell fitness are equal.

Gene regulatory network

A gene or genetic regulatory network GRN is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the function of the cell. GRN also play a central role in morphogenesis , the creation of body structures, which in turn is central to evolutionary developmental biology evo-devo. The interaction can be direct or indirect through transcribed RNA or translated protein. In general, each mRNA molecule goes on to make a specific protein or set of proteins. In some cases this protein will be structural , and will accumulate at the cell membrane or within the cell to give it particular structural properties.


To address topological properties of these two networks, we quantified correlations between connectivities of interacting nodes and compared.


Constructing transcriptional regulatory networks

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Studies of the yeast protein interaction network have revealed distinct correlations between the connectivity of individual proteins within the network and the average connectivity of their neighbours. Although a number of biological mechanisms have been proposed to account for these findings, the significance and influence of the specific datasets included in these studies has not been appreciated adequately. We show how the use of different interaction data sets, such as those resulting from high-throughput or small-scale studies, and different modelling methodologies for the derivation pair-wise protein interactions, can dramatically change the topology of these networks.

All course materials in Train online are free cultural works licensed under a Creative Commons Attribution-ShareAlike 4. Get help and support. It is also essential in drug development, since drugs can affect PPIs. These contacts:.

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In this issue, Leandrou et al. Kinase activity was notably different in mutant LRRK2 hetero- and homo-dimers. The cover image shows that de-phosphorylated and mutant LRRK2 cytoplasmic filaments are comprised of dimeric species.

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