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Data_availability.pdf [article]

Natalia Sanchez De Groot, Alexandros Armaos, Ricardo Graña, Marion Alriquet, Giulia Calloni, R. Martin Vabulas, Gian Gaetano Tartaglia
<span title="2019-05-15">2019</span> <i title="Figshare"> Figshare </i> &nbsp;
List of submission links to results from "RNA structure drives protein interaction"
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.8131883">doi:10.6084/m9.figshare.8131883</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4afk3pmh4jdajjt4pinnzoni2i">fatcat:4afk3pmh4jdajjt4pinnzoni2i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200214041232/https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/15168881/Data_availability.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f6/a6/f6a6abb5062411cf96262ae5c9af0a69e7df4167.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.8131883"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> figshare.com </button> </a>

The Grand Challenge of Characterizing Ribonucleoprotein Networks

Gian Gaetano Tartaglia
<span title="2016-06-09">2016</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zqzewb742bdglfxhkef3ke6cla" style="color: black;">Frontiers in Molecular Biosciences</a> </i> &nbsp;
Protein-RNA interactions are at the heart of cell regulation. From transcription, processing, storage, and translation, all the stages in the life cycle of an RNA depend on interactions with proteins. Although technologies are making remarkable progress in unraveling the landscape of protein-RNA interactions, many key issues are unclear. We still have to identify how many proteins have RNA-binding ability, what are their targets and functional pathways. Moreover, while we know the number of
more &raquo; ... ein-coding genes in the human genome, functional non-coding RNAs are still poorly defined. What is the function of the non-coding part of the eukaryotic transcriptome? A clear understanding of the biological functions of coding and non-coding transcripts would provide novel insights in molecular biology. What are the protein components binding to an RNA while it is being produced? Our lack of understanding of how ribonucleoprotein complexes assemble is a major rate-limiting factor to future progress in the field. We need to generate an in-depth characterization of protein-RNA complexes that form in cells during development and in response to external stimuli. Life on earth might descend from an RNA world (Higgs and Lehman, 2015) although RNA and proteins could have emerged together. As protein-based molecules are essential to make nucleic acid polymers and nucleotide-based molecules are needed to synthesize proteins, protein, and RNA might have co-evolved from the very beginning of life (Chao et al., 2008) : RNA would contain the instructions for life while peptides accelerate key chemical reactions to carry out the instructions. In support of this hypothesis, it has been reported that network of reactions beginning with hydrogen cyanide and hydrogen sulfide in streams of water irradiated by UV light could produce the chemical components of proteins and lipids, alongside those of RNA (Patel et al., 2015).
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmolb.2016.00024">doi:10.3389/fmolb.2016.00024</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27376072">pmid:27376072</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4899450/">pmcid:PMC4899450</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wqr6oxcbmrcxpnxighjwzj5en4">fatcat:wqr6oxcbmrcxpnxighjwzj5en4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200310194744/https://repositori.upf.edu/bitstream/handle/10230/30885/Tartaglia_frontiersmb_gran.pdf;jsessionid=0612A80EF9F28B1E25B9484D07643A28?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ed/36/ed36103acd45cb250ca58c6e7fefe5ca1fda3f99.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmolb.2016.00024"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899450" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Long non-coding RNA-polycomb intimate rendezvous

Andrea Cerase, Gian Gaetano Tartaglia
<span title="2020-09-09">2020</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4j4bwhj4vzfjbnjfg5bmk3mnk4" style="color: black;">Open Biology</a> </i> &nbsp;
We thank all members of the Tartaglia and Cerase's laboratories. We also thank Roberto Bonasio and Chen Davidovich, Giacomo Cavalli and John Rinn for helpful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsob.200126">doi:10.1098/rsob.200126</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32898472">pmid:32898472</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/po5udlbivnatdea5zpjislg76m">fatcat:po5udlbivnatdea5zpjislg76m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210716220718/https://repositori.upf.edu/bitstream/handle/10230/45698/Cerase_ob_long.pdf;jsessionid=06787FBFA69648E509C7645D3C84B27C?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cf/0d/cf0d9bd92dd9cc85c98c604fb9adfec730dc2607.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsob.200126"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Aggregation is a context-dependent constraint on protein evolution [article]

Michele Monti, Alexandros Armaos, Marco Fantini, Annalisa Pastore, Gian Gaetano Tartaglia
<span title="2021-05-11">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Solubility is a requirement for many cellular processes. Loss of solubility and aggregation can lead to the partial or complete abrogation of protein function. Thus, understanding the relationship between protein evolution and aggregation is an important goal. Here, we analysed two deep mutational scanning experiments to investigate the role of protein aggregation in molecular evolution.In one data set, mutants of a protein involved in RNA biogenesis and processing, human TAR DNA binding
more &raquo; ... 43 (TDP-43), were expressed inS. cerevisiae. In the other data set, mutants of a bacterial enzyme that controls resistance to penicillins and cephalosporins, TEM-1 beta-lactamase, were expressed inE. coli under the selective pressure of an antibiotic treatment. We found that aggregation differentiates the effects of mutations in the two different cellular contexts. Specifically, aggregation was found to be associated with increased cell fitness in the case of TDP-43 mutations, as it protects the host from aberrant interactions. By contrast, in the case of TEM-1 beta-lactamase mutations, aggregation is linked to a decreased cell fitness due to inactivation of protein function.Our study shows that aggregation is an important context-dependent constraint of molecular evolution and opens up new avenues to investigate the role of aggregation in different cellular contexts-
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.10.443436">doi:10.1101/2021.05.10.443436</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/khiuxpyvdbewbbkvaj4l5p6uzi">fatcat:khiuxpyvdbewbbkvaj4l5p6uzi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210717081613/https://www.biorxiv.org/content/biorxiv/early/2021/05/11/2021.05.10.443436.1.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/72/35/723506ca77cae34858b316dae19f874583e32db1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.10.443436"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Discovery of protein–RNA networks

Davide Cirillo, Carmen Maria Livi, Federico Agostini, Gian Gaetano Tartaglia
<span title="">2014</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zcnlz4nminfhjcp5esifetrr4u" style="color: black;">Molecular Biosystems</a> </i> &nbsp;
The findings of this analysis can be summarized as follows: Gian Gaetano Tartaglia High nitrogen content and high isoelectric point discriminate RBPs from other proteins.  ...  Gian Gaetano Tartaglia received his MPhil in Theoretical Physics from the University of Rome La Sapienza in 2000 (Italy) with a thesis on mathematical modeling of neurons.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c4mb00099d">doi:10.1039/c4mb00099d</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24756571">pmid:24756571</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hmdr6ox7yjdybgthvcqvf5i3k4">fatcat:hmdr6ox7yjdybgthvcqvf5i3k4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809085020/http://s.tartaglialab.com/static_files/shared/Cirillo_MB_2014.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ac/e0/ace02d0a9b2a3b87dc6e42b557cec3d2c41cec00.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c4mb00099d"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Physicochemical Principles of Protein Aggregation [chapter]

Benedetta Bolognesi, Gian Gaetano Tartaglia
<span title="">2013</span> <i title="Elsevier"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iiku6qaq6rd4lcpnbevlkv35ze" style="color: black;">Progress in Molecular Biology and Translational Science</a> </i> &nbsp;
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/b978-0-12-386931-9.00003-9">doi:10.1016/b978-0-12-386931-9.00003-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23663965">pmid:23663965</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uk722o2rx5gifkqcrv2emob4im">fatcat:uk722o2rx5gifkqcrv2emob4im</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160818074519/http://service.tartaglialab.com/static_files/shared/Bolognesi_Progress.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f5/ac/f5aca54ca3158040dab0df3c36f349cce06552da.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/b978-0-12-386931-9.00003-9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

The mutational landscape of a prion-like domain [article]

Benedetta Bolognesi, Andre J. Faure, Mireia Seuma, Jörn M. Schmiedel, Gian Gaetano Tartaglia, Ben Lehner
<span title="2019-03-31">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
AbstractSpecific insoluble protein aggregates are the hallmarks of many neurodegenerative diseases1–5. For example, cytoplasmic aggregates of the RNA-binding protein TDP-43 are observed in 97% of cases of Amyotrophic Lateral Sclerosis (ALS)6,7. However, it is still unclear for ALS and other diseases whether it is the insoluble aggregates or other forms of the mutated proteins that cause these diseases that are actually toxic to cells8–13. Here we address this question for TDP-43 by
more &raquo; ... y mutating14 the protein and quantifying the effects on cellular toxicity. We generated >50,000 mutations in the intrinsically disordered prion-like domain (PRD) and observed that changes in hydrophobicity and aggregation potential are highly predictive of changes in toxicity. Surprisingly, however, increased hydrophobicity and cytoplasmic aggregation actually reduce cellular toxicity. Mutations have their strongest effects in a central region of the PRD, with variants that increase toxicity promoting the formation of more dynamic liquid-like condensates. The genetic interactions in double mutants reveal that specific structures exist in this 'unstructured' region in vivo. Our results demonstrate that deep mutagenesis is a powerful approach for probing the sequence-function relationships of intrinsically disordered proteins as well as their in vivo structural conformations. Moreover, we show that aggregation of TDP-43 is not harmful but actually protects cells, most likely by titrating the protein away from a toxic liquid-like phase.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/592121">doi:10.1101/592121</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/35ckcvodbbb7vlgiypxu62tjhe">fatcat:35ckcvodbbb7vlgiypxu62tjhe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429104837/https://www.biorxiv.org/content/biorxiv/early/2019/03/31/592121.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a0/33/a033ab09e11764c44a117e243e943c33c965a930.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/592121"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

A Computational Approach for the Discovery of Protein–RNA Networks [chapter]

Domenica Marchese, Carmen Maria Livi, Gian Gaetano Tartaglia
<span title="">2016</span> <i title="Springer New York"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
Protein-RNA interactions play important roles in a wide variety of cellular processes, ranging from transcriptional and post-transcriptional regulation of genes to host defense against pathogens. In this chapter we present the computational approach catRAPID to predict protein-RNA interactions and discuss how it could be used to find trends in ribonucleoprotein networks. We envisage that the combination of computational and experimental approaches will be crucial to unravel the role of coding and non-coding RNAs in protein networks
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-3067-8_2">doi:10.1007/978-1-4939-3067-8_2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26463375">pmid:26463375</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ckx2gnus7jfqlmrfhz5fbxp4ze">fatcat:ckx2gnus7jfqlmrfhz5fbxp4ze</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721032942/https://repositori.upf.edu/bitstream/handle/10230/32301/March_Met_Com.pdf;jsessionid=BAD17AB35587198E8D1A78B51F012BC0?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ff/bd/ffbdadff93548115b34b778b6e73cf505cf7d349.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-3067-8_2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Neurodegeneration and Cancer: Where the Disorder Prevails

Petr Klus, Davide Cirillo, Teresa Botta Orfila, Gian Gaetano Tartaglia
<span title="2015-10-23">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
It has been reported that genes up-regulated in cancer are often down-regulated in neurodegenerative disorders and vice versa. The fact that apparently unrelated diseases share functional pathways suggests a link between their etiopathogenesis and the properties of molecules involved. Are there specific features that explain the exclusive association of proteins with either cancer or neurodegeneration? We performed a large-scale analysis of physico-chemical properties to understand what
more &raquo; ... ristics differentiate classes of diseases. We found that structural disorder significantly distinguishes proteins up-regulated in neurodegenerative diseases from those linked to cancer. We also observed high correlation between structural disorder and age of onset in Frontotemporal Dementia, Parkinson's and Alzheimer's diseases, which strongly supports the role of protein unfolding in neurodegenerative processes. It has been reported that tumor suppressor p53 has physico-chemical features that are typical of prionoid proteins associated with neurodegenerative diseases 1 . This finding is particularly interesting because it suggests that common molecular properties can be linked to relatively distant diseases. As a matter of fact, a recent study by Ibáñez et al. 2 shows that transcripts up-regulated in cancer are down-regulated in central nervous system (CNS) diseases and vice versa. In line with this finding, a risk reduction for some cancer types has been observed in patients affected by Parkinson's 3 and Alzheimer's diseases 4 . Are there common physico-chemical determinants behind comorbidities? We re-analysed the data published by Ibáñez et al. 2 to understand if differential regulation of genes can be associated with specific protein features. While the original study by Ibáñez et al. 2 focused on transcripts that are exclusively up-regulated in cancer and down-regulated in CNS diseases and vice versa 2 , our analysis deals with genes that are exclusively associated with either CNS diseases or cancer (Fig. 1 ). In agreement with recent experimental findings 5 and theoretical analyses 6-9 , we investigated the physico-chemical properties of gene products assuming a proportionality between transcript and protein abundances.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep15390">doi:10.1038/srep15390</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26493371">pmid:26493371</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4615981/">pmcid:PMC4615981</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fogi353a4ngatdnxv2ord6vewq">fatcat:fogi353a4ngatdnxv2ord6vewq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200314165527/https://www.nature.com/articles/srep15390.pdf?error=cookies_not_supported&amp;code=dfedcb3c-64ca-4bc1-9383-eef9451a734b" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/72/bb/72bb3eea59743a4af39a200ee21c5b606fb09d9b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep15390"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615981" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Zyggregator method for predicting protein aggregation propensities

Gian Gaetano Tartaglia, Michele Vendruscolo
<span title="">2008</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qoebttzoxbfgviecxmhjrua4eu" style="color: black;">Chemical Society Reviews</a> </i> &nbsp;
These factors were included in an equation to correlate the changes in aggregation rates relative to the wild-type protein for single substitutions in regions of Gian Gaetano Tartaglia studied theoretical  ...  described in eqn (1), the TANGO method considers explicitly the enthalpic and entropic costs associated to the conformational transition between folded and aggregated structures, 7 and the method by Tartaglia  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/b706784b">doi:10.1039/b706784b</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18568165">pmid:18568165</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mfaicy5nlre47ab6swqxm6wwca">fatcat:mfaicy5nlre47ab6swqxm6wwca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810003215/http://www-vendruscolo.ch.cam.ac.uk/tartaglia08csr.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b5/ce/b5ce4f265f58dd818de72e252b7f5daf28afb821.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/b706784b"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Neurodegeneration as an RNA disorder

Rory Johnson, Wendy Noble, Gian Gaetano Tartaglia, Noel J. Buckley
<span title="2012-10-10">2012</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fptky5bef5gmpjh2fugyz6i3yq" style="color: black;">Progress in Neurobiology</a> </i> &nbsp;
Neurodegenerative diseases constitute one of the single most important public health challenges of the coming decades, and yet we presently have only a limited understanding of the underlying genetic, cellular and molecular causes. As a result, no effective disease-modifying therapies are currently available, and no method exists to allow detection at early disease stages, and as a result diagnoses are only made decades after disease pathogenesis, by which time the majority of physical damage
more &raquo; ... s already occurred. Since the sequencing of the human genome, we have come to appreciate that the transcriptional output of the human genome is extremely rich in non-protein coding RNAs (ncRNAs). This heterogeneous class of transcripts is widely expressed in the nervous system, and is likely to play many crucial roles in the development and functioning of this organ. Most exciting, evidence has recently been presented that ncRNAs play central, but hitherto unappreciated roles in neurodegenerative processes. Here, we review the diverse available evidence demonstrating involvement of ncRNAs in neurodegenerative diseases, and discuss their possible implications in the development of therapies and biomarkers for these conditions.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.pneurobio.2012.09.006">doi:10.1016/j.pneurobio.2012.09.006</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23063563">pmid:23063563</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7116994/">pmcid:PMC7116994</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k6dr4ciffjdj3hb3wpltwn4kzu">fatcat:k6dr4ciffjdj3hb3wpltwn4kzu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160818092329/http://service.tartaglialab.com/static_files/shared/Johnson_Prog%20Neurobio_2012.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/70/cf/70cf238eac83d9feee1bd80e0aeb888ab2465e24.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.pneurobio.2012.09.006"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116994" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Predicting protein associations with long noncoding RNAs

Matteo Bellucci, Federico Agostini, Marianela Masin, Gian Gaetano Tartaglia
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/l6cw2tyvgrhytbvantrj2os37y" style="color: black;">Nature Methods</a> </i> &nbsp;
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nmeth.1611">doi:10.1038/nmeth.1611</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21623348">pmid:21623348</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pepwwi4cobgufoz5zqxv2bivvm">fatcat:pepwwi4cobgufoz5zqxv2bivvm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160818090443/http://service.tartaglialab.com/static_files/shared/Bellucci_NatMethods_Suppl_2011.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/99/6a/996a9c110f54030eca873375bbaf62f3d0d0eb9c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nmeth.1611"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a>

Sequence-Based Prediction of Protein Solubility

Federico Agostini, Michele Vendruscolo, Gian Gaetano Tartaglia
<span title="">2012</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nk6zopmzsjfizb6z5kztdu477y" style="color: black;">Journal of Molecular Biology</a> </i> &nbsp;
In order to investigate the relationship between the thermodynamics and kinetics of protein aggregation, we compared the solubility of proteins with their aggregation rates. We found a significant correlation between these two quantities by considering a database of protein solubility values measured using an in vitro reconstituted translation system containing about 70% of Escherichia coli proteins. The existence of such correlation suggests that the thermodynamic stability of the native
more &raquo; ... of proteins relative to the aggregate states is closely linked with the kinetic barriers that separate them. In order to create the possibility of conducting computational studies at the proteome level to investigate further this concept, we developed a method of predicting the solubility of proteins based on their physicochemical properties. Crown
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2011.12.005">doi:10.1016/j.jmb.2011.12.005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22172487">pmid:22172487</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r3aq7dtghbdt3myv27vxr6wkna">fatcat:r3aq7dtghbdt3myv27vxr6wkna</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170705131800/http://www-vendruscolo.ch.cam.ac.uk/agostini12jmb.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8a/71/8a71739badc99f1556bff85c76e506a0808de894.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2011.12.005"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Physicochemical Determinants of Chaperone Requirements

Gian Gaetano Tartaglia, Christopher M. Dobson, F. Ulrich Hartl, Michele Vendruscolo
<span title="">2010</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nk6zopmzsjfizb6z5kztdu477y" style="color: black;">Journal of Molecular Biology</a> </i> &nbsp;
We describe a series of stringent relationships between abundance, solubility and chaperone usage of proteins. Based on these relationships, we show that the need of Escherichia coli proteins for the chaperonin GroEL can be predicted with 86% accuracy. Furthermore, from the observation that the abundance and solubility of proteins depend on the physicochemical properties of their amino acid sequences, we demonstrate that the requirement for GroEL can also be predicted directly from the
more &raquo; ... with 90% accuracy. These results indicate that the physicochemical properties of the amino acid sequences represent an essential component of the cellular quality control system that ensures the maintenance of protein homeostasis in living systems.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2010.03.066">doi:10.1016/j.jmb.2010.03.066</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20416322">pmid:20416322</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/22lb3xkgorehraux7zcybkwffi">fatcat:22lb3xkgorehraux7zcybkwffi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808042821/http://www-vendruscolo.ch.cam.ac.uk/papers/groel.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/03/f6/03f65331c876017b78d27065085e2ff6f7800c7a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2010.03.066"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

catRAPIDsignature: identification of ribonucleoproteins and RNA-binding regions

Carmen Maria Livi, Petr Klus, Riccardo Delli Ponti, Gian Gaetano Tartaglia
<span title="2015-10-31">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Motivation: Recent technological advances revealed that an unexpected large number of proteins interact with transcripts even if they lack annotated RNA-binding domains. We introduce catRAPID signature to identify ribonucleoproteins based on physico-chemical features instead of sequence similarity searchers. The algorithm, trained on human proteins and tested on model organisms, calculates the overall RNA-binding propensity followed by the prediction of RNA-binding regions. catRAPID signature
more &raquo; ... tperforms other algorithms in the identification of RNA-binding proteins and detection of non-classical RNA-binding regions. Results are visualized on a webpage and can be downloaded or forwarded to catRAPID omics for predictions of RNA targets. Availability and implementation: catRAPID signature can be accessed at http://s.tartaglialab.com/new_submission/signature Supplementary information: Supplementary data are available at Bioinformatics online and at the online Documentation and Tutorial.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btv629">doi:10.1093/bioinformatics/btv629</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26520853">pmid:26520853</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4795616/">pmcid:PMC4795616</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n2aykgtr3nbe3jqmg5bxpbe47q">fatcat:n2aykgtr3nbe3jqmg5bxpbe47q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808041531/http://public-files.prbb.org/publicacions/4f505960-63a5-0133-59f6-525400e56e78.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6a/51/6a5160e55dac11e71909dade41654df7f515cb3f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btv629"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795616" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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