http://precedings.nature.com/tags/protein%20interactions Recently posted documents tagged with 'protein interactions' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/2041/version/1 A compilation of experimentally verified interactions between HIV-1 and human proteins allows insights into the intricate interplay between viral and host proteins on a large scale.We find that HIV-1 predominantly targets rich-clubs, human proteins that are not only well connected but also strongly intertwined among each other. These assemblies of proteins putatively serve as an infection gateway, allowing the virus to take control of the human host by reaching protein pathways and diversified cellular functions in a pronounced and focused way. In particular, HIV-1 utilizes its small number of proteins in a combinatorial manner, exerting a significant influence on pathways that deal with transcriptional, translational and degradation processes. Surprisingly, the small repertoire of HIV proteins also interferes loosely with many signaling and regulation pathways, suggesting that a widespread involvement in such pathways secures the control of the host cell. Such insights offer novel perspectives to investigate the progression of HIV infection and potentially can contribute to our abilities to fight this virus. http://precedings.nature.com/documents/2041/version/1 Wed, 09 Jul 2008 17:18:11 UTC Viral organization of human proteins hdl:10101/npre.2008.2041.1 2008-07-09 Stefan Wuchty Nature Precedings 2008-07-09T17:18:11Z Manuscript Microbiology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1522/version/2 The accurate description and analysis of protein-protein interfaces remains a challenging task. Traditional definitions, based on atomic contacts or changes in solvent accessibility, tend to over- or underpredict the interface itself and cannot discriminate active from less relevant parts.We here extend a fast, parameter-free and purely geometric definition of protein interfaces and introduce the shelling order of Voronoi facets as a novel measure for an atom’s depth inside the nterface. Our analysis of 54 protein-protein complexes reveals a strong correlation between Voronoi Shelling Order (VSO) and water dynamics. High Voronoi Shelling Order coincides with residues that were found shielded from bulk water fluctuations in a recent molecular dynamics study. Yet, VSO predicts such “dry” residues at dramatically reduced cost and without consideration of forcefields or dynamics. More central interface positions are often also increasingly enriched for hydrophobic residues. Yet, this hydrophobic centering is not universal and does not mirror the far stronger geometric bias of water fluxes. The seemingly complex water dynamics at protein interfaces appears thus largely controlled by geometry. Sequence analysis supports the functional relevance of both dry residues and residues with high VSO, both of which tend to be more conserved. However, upon closer inspection, the spatial distribution of conservation argues against the arbitrary dissection into core or rim and thus refines previous results. Voronoi Shelling Order reveals clear geometric patterns in protein interface composition, function and dynamics and facilitates the comparative analysis of protein-protein interactions. http://precedings.nature.com/documents/1522/version/2 Mon, 23 Jun 2008 14:19:00 UTC Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation hdl:10101/npre.2008.1522.2 2008-06-23 Raik Grünberg Nature Precedings 2008-06-23T14:19:00Z Manuscript Chemistry Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1522/version/1 The accurate description of protein-protein interfaces remains a challenging task. Traditional criteria, based on atomic contacts or changes in solvent accessibility, tend to over or underpredict the interface itself and cannot discriminate active from less relevant parts. A recent simulation study by Mihalek and co-authors (2007, JMB 369, 584-95) concluded that active residues tend to be `dry’, that is, insulated from water fluctuations. We show that patterns of `dry’ residues can, to a large extent, be predicted by a fast, parameter-free and purely geometric analysis of protein interfaces. We introduce the shelling order of Voronoi facets as a straightforward quantitative measure of an atom’s depth inside an interface. We analyze the correlation between Voronoi shelling order, dryness, and conservation on a set of 54 protein-protein complexes. Residues with high shelling order tend to be dry; evolutionary conservation also correlates with dryness and shelling order but, perhaps not surprisingly, is a much less accurate predictor of either property. Voronoi shelling order thus seems a meaningful and efficient descriptor of protein interfaces. Moreover, the strong correlation with dryness suggests that water dynamics within protein interfaces may, in first approximation, be described by simple diffusion models. http://precedings.nature.com/documents/1522/version/1 Wed, 16 Jan 2008 17:21:30 UTC Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation hdl:10101/npre.2008.1522.1 2008-01-16 Raik Grünberg Nature Precedings 2008-01-16T17:21:30Z Manuscript Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.196.1 Dystroglycan is part of a large complex of proteins, the dystrophin-glycoprotein complex, which has been implicated in the pathogenesis of muscular dystrophies for a long time. Besides muscular degeneration many patients manifest symptoms of neurological and cognitive dysfunction. Newer findings suggest that dystroglycan is implicated in brain development, synapse formation and plasticity, nerve-glia interactions and maintenance of the blood-brain barrier.Most research so far has focused on the functions of dystroglycan in muscle and neuromuscular junctions, while its role in the brain and interneuronal synapses has been largely neglected. This review will give an overview of the biochemistry of dystroglycan, its interaction with other proteins as well as its confirmed and hypothetical functions in the nervous system in health and diesease. http://dx.doi.org/10.1038/npre.2007.196.1 Tue, 26 Jun 2007 05:07:06 UTC Review: Dystroglycan in the Nervous System doi:10.1038/npre.2007.196.1 2007-06-26 Matthias Samwald Nature Precedings 2007-06-26T05:07:06Z Manuscript Neuroscience http://creativecommons.org/licenses/by/2.5/ http://dx.doi.org/10.1038/npre.2007.22.1 It has been previously shown [1] that S. cerevisiae proteins preferentially interact with proteins of the same estimated likely time of origin. To study this observation further, the protein interaction networks of S. cerevisiae and H. sapiens were analyzed taking into account an estimate for the age of the proteins in these species. These estimates were obtained by studying the presence and absence of putative orthologs in other eukaryotic species. In this work preliminary results are described that point to a dependence of the likelihood of protein interaction on the proteins’ age. The probability of two proteins interactions was found to be linearly dependent on the time the proteins have co-existed in the species. http://dx.doi.org/10.1038/npre.2007.22.1 Mon, 22 Jan 2007 16:50:37 UTC The likelihood that two proteins interact might depend on the proteins’ age doi:10.1038/npre.2007.22.1 2009-03-04 Pedro Beltrao Nature Precedings 2007-01-22T16:50:37Z Manuscript Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/2.5/