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Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs

Tien-Ho Lin, Ziv Bar-Joseph, Robert F. Murphy
2011 Journal of Computational Biology  
We first develop a system that utilizes the known cellular sorting pathways to learn sequence motifs and predict locations.  ...  This thesis introduces new computational methods that extract these sequence motifs and carrier proteins, and learn the sorting pathways.  ...  We first develop a system that utilizes the known cellular sorting pathways to learn sequence motifs and predict locations.  ... 
doi:10.1089/cmb.2011.0193 pmid:21999284 pmcid:PMC3216107 fatcat:fzqi5tdydbgb5jkwc7oqjexjuu

Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs [chapter]

Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy
2011 Lecture Notes in Computer Science  
We first develop a system that utilizes the known cellular sorting pathways to learn sequence motifs and predict locations.  ...  This thesis introduces new computational methods that extract these sequence motifs and carrier proteins, and learn the sorting pathways.  ...  We first develop a system that utilizes the known cellular sorting pathways to learn sequence motifs and predict locations.  ... 
doi:10.1007/978-3-642-20036-6_20 fatcat:jc2zx6wmrzbzjgiczc6pcosn7e

Mechanisms of enveloped RNA virus budding

Owen Pornillos, Jennifer E Garrus, Wesley I Sundquist
2002 Trends in Cell Biology  
Recent research indicates that HIV and other enveloped RNA viruses bud by appropriating the cellular machinery that is normally used to create vesicles that bud into late endosomal compartments called  ...  This new model of virus budding has many potential implications for cell biology and viral pathogenesis.  ...  Acknowledgements We thank Paul Bieniasz, Scott Emr, Heinrich Göttlinger, Ron Harty, Dan Higginson, Bob Lamb, Mark Marsh, Graça Raposo and  ... 
doi:10.1016/s0962-8924(02)02402-9 pmid:12495845 fatcat:mcbhxn7wrrbb5igsouosthpbmi

How megalin finds its way: identification of a novel apical sorting motif. Focus on "Identification of an apical sorting determinant in the cytoplasmic tail of megalin"

Michael J. Caplan
2003 American Journal of Physiology - Cell Physiology  
Megalin spans the membrane once, and its cytoplasmic COOH terminus possesses a wealth of sequences that resemble motifs involved in sorting or in various types of protein-protein interactions (15, 34)  ...  Much remains to be learned about the nature of the sorting information that spec-ifies each protein's subcellular localization and about the cellular sorting apparatus that interprets and acts upon this  ... 
doi:10.1152/ajpcell.00004.2003 pmid:12676652 fatcat:gpr4k4njq5cb7cisko5eni2yq4

Plasma Membrane-Associated Restriction Factors and Their Counteraction by HIV-1 Accessory Proteins

Ramirez, Sharma, Singh, Stoneham, Vollbrecht, Guatelli
2019 Cells  
Here we review key features of these two antiviral proteins, and we review Vpu and Nef, which deplete them from the plasma membrane by co-opting specific cellular proteins and pathways of membrane trafficking  ...  and protein-degradation.  ...  Funding: This work was supported by grants from the National Institutes of Health: R37AI081668 and R01AI129706. P.W.R. was partly supported by NIH grant K12GM068524.  ... 
doi:10.3390/cells8091020 pmid:31480747 pmcid:PMC6770538 fatcat:4n5hyazszbf27bk7eeegtz6sza

Neurotrophins: A Ticket to Ride for BDNF

Kerrie Thomas, Alun Davies
2005 Current Biology  
A recent study by Lou et al. [8] highlights the importance of the interaction of a highly conformation-dependent sorting signal in the tertiary structure of BDNF with the sorting receptor carboxypeptidase  ...  Secreted proteins transit the Golgi apparatus to the trans-Golgi network where two kinds of secretory vesicle are generated: those of the constitutive pathway are transported to and fuse with the plasma  ...  In addition to the sorting motif in mature BDNF, the proBDNF sequence also influences sorting.  ... 
doi:10.1016/j.cub.2005.03.023 pmid:15823529 fatcat:3jeoush33jchvc44u7kvam3r6q

Page 2204 of The Journal of Neuroscience Vol. 22, Issue 6 [page]

2002 The Journal of Neuroscience  
The RRK*’’-*” tripeptide could be recognized during sorting, re- quired for retention at specific sites, or involved in interactions with the cytoskeleton; the identification of interacting proteins should  ...  Neurons may use several distinct mechanisms to achieve sub- cellular compartmentalization of synaptic components.  ... 

Functional roles of short sequence motifs in the endocytosis of membrane receptors

Kailash, N. Pandey
2009 Frontiers in Bioscience  
The signals usually consist of short linear amino acid sequences, which are recognized by adaptor coat proteins along the endocytic and sorting pathways.  ...  The specific characteristics and functions of short-sequence motifs, including various tyrosine-based, dileucine-type, and other short-sequence signals in the trafficking and sorting of membrane receptors  ...  Indeed, the function of short-sequence signal motifs in protein-protein interactions among all the trafficking pathways of specific membrane receptors and proteins remains to be established.  ... 
doi:10.2741/3599 pmid:19482617 pmcid:PMC2751658 fatcat:jzejukjfnneddlx252liy4bpyi

Small peptide recognition sequence for intracellular sorting

Kailash N Pandey
2010 Current Opinion in Biotechnology  
The short signals usually consist of small linear amino acid sequences, which are recognized by adaptor coat proteins along the endocytic and sorting pathways.  ...  compartments, however, the significance and scope of the short sequence motifs in these cellular events is not well understood.  ...  [PubMed: 11914729] **The targeting and sorting of individual receptor and / or membrane proteins is directed by their intrinsic sequence-based signal motifs in the endocytotic and secretory pathways,  ... 
doi:10.1016/j.copbio.2010.08.007 pmid:20817434 pmcid:PMC2997389 fatcat:osshqhwonzhzhc3bk4qhvgzhlu

SARS-CoV-2 contributes to altering the post-transcriptional regulatory networks across human tissues by sponging RNA binding proteins and micro-RNAs [article]

Rajneesh Srivastava, Swapna Vidhur Daulatabad, Mansi Srivastava, Sarath Chandra Janga
2020 biorxiv/medrxiv  
Motif enrichment analysis on the RNA genomic sequence of SARS-CoV-2 clearly revealed an enrichment for RBPs such as SRSFs, PCBPs, ELAVs and HNRNPs illustrating the sponging of RBPs by SARS-CoV-2 genome  ...  We uncovered that 13 out of 29 SARS-CoV- 2 encoded proteins directly interact with 51 human RBPs of which majority of them were abundantly expressed in gonadal tissues and immune cells.  ...  Acknowledgments: We thank the lab members for their valuable suggestions and the supporting dataset required for completion of this project.  ... 
doi:10.1101/2020.07.06.190348 pmid:32676599 pmcid:PMC7359521 fatcat:7faikq75p5bunjckehco5ko4aa

Synthetic modular systems - reverse engineering of signal transduction

Tony Pawson, Rune Linding
2005 FEBS Letters  
Designing and successfully introducing synthetic proteins into cellular pathways would provide us with a powerful research tool with many applications, such as development of biosensors, protein drugs  ...  ., proteins and genes). This has generated a considerable amount of knowledge and hypotheses concerning cellular organization.  ...  These synthetic proteins could function as control units (gates and switches) that allow for switching and gating in cellular or in vitro systems, thus allowing us to rewire or probe signaling pathways  ... 
doi:10.1016/j.febslet.2005.02.013 pmid:15763556 fatcat:eg7dadryfvdbtkg2pmhagsuswq

Assembly of Cell Regulatory Systems Through Protein Interaction Domains

T. Pawson
2003 Science  
The regulation of many different cellular processes requires the use of protein interaction domains to direct the association of polypeptides with one another and with phospholipids, small molecules, or  ...  The sequencing of complete genomes provides a list that includes the proteins responsible for cellular regulation.  ...  of endowing cells with new properties by using protein interactions to respecify signaling pathways.  ... 
doi:10.1126/science.1083653 pmid:12702867 fatcat:xcxokrazjnch5kvbkf7jou33iy

After Hrs with HIV

Ali Amara, Dan R. Littman
2003 Journal of Cell Biology  
They surveyed Vps proteins for the PTAP or PSAP sequences present in p6 and found such a motif in Hrs.  ...  To efficiently bud off from infected cells, HIV and other enveloped viruses hijack the host cellular machinery that is normally involved in vacuolar protein sorting and multivesicular body (MVB) biogenesis  ... 
doi:10.1083/jcb.200307062 pmid:12900390 pmcid:PMC2172700 fatcat:wxyxmrm62neozmbin6p22wxf3e

Subcellular Trafficking of Mammalian Lysosomal Proteins: An Extended View

Catherine Staudt, Emeline Puissant, Marielle Boonen
2016 International Journal of Molecular Sciences  
Lysosomes clear macromolecules, maintain nutrient and cholesterol homeostasis, participate in tissue repair, and in many other cellular functions.  ...  In addition, several "non-consensus" sorting motifs have been identified, and atypical transport routes to endolysosomes have been brought to light.  ...  Author Contributions: Marielle Boonen, Emeline Puissant, and Catherine Staudt wrote the article. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms18010047 pmid:28036022 pmcid:PMC5297682 fatcat:ssdup7vsvzaoth36lzi32fl7tu

Role of SARS-CoV-2 in Altering the RNA-Binding Protein and miRNA-Directed Post-Transcriptional Regulatory Networks in Humans

Rajneesh Srivastava, Swapna Vidhur Daulatabad, Mansi Srivastava, Sarath Chandra Janga
2020 International Journal of Molecular Sciences  
A motif enrichment analysis on the RNA genomic sequence of SARS-CoV-2 clearly revealed the enrichment for RBPs such as SRSFs, PCBPs, ELAVs, and HNRNPs, suggesting the sponging of RBPs by the SARS-CoV-2  ...  We uncovered that 13 out of 29 SARS-CoV-2-encoded proteins directly interacted with 51 human RBPs, of which the majority of them were abundantly expressed in gonadal tissues and immune cells.  ...  Acknowledgments: We thank the lab members for their valuable suggestions and the supporting dataset required for completion of this project.  ... 
doi:10.3390/ijms21197090 pmid:32993015 fatcat:id3vb52xbjcwhazashv5u4pa7y
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