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GlobPlot: exploring protein sequences for globularity and disorder

R. Linding
2003 Nucleic Acids Research  
GlobPlot (http:// globplot.embl.de) is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder.  ...  Thus GlobPlot may be of use in the design of constructs corresponding to globular proteins, as needed for many biochemical studies, particularly structural biology.  ...  ACKNOWLEDGEMENTS We thank Will Stanley, Kresten Lindorff-Larsen, Jesper Borg and David Martin for cool fruitful discussions and suggestions and Christine Gemuend and Ivica Letunic for SMART interface code  ... 
doi:10.1093/nar/gkg519 pmid:12824398 pmcid:PMC169197 fatcat:4m6yrykpkfbe3m6pw6t6fmh5ee

N- and C-Terminal Truncations to Enhance Protein Solubility and Crystallization: Predicting Protein Domain Boundaries with Bioinformatics Tools [chapter]

Christopher D. O. Cooper, Brian D. Marsden
2017 Msphere  
Soluble protein expression is a key requirement for biochemical and structural biology approaches to study biological systems in vitro.  ...  Determination of such protein domain boundaries can be challenging for novel proteins.  ...  (d) GlobPlot graphical output for full-length POLQ as query sequence. Globular domains are green blocks, disordered regions as blue blocks and recognized SMART domains according to the key.  ... 
doi:10.1007/978-1-4939-6887-9_2 pmid:28470596 fatcat:5yz6vhni4jadbeqhcbuvibi5j4

Computational Analysis of Modular Protein Architectures [chapter]

Rune Linding, Ivica Letunic, Toby J. Gibson, Peer Bork
2005 Modular Protein Domains  
Thanks to Kresten Lindorff-Larsen, Sophie Chabanis-Davidson, Sara Quirk, and Francesca Diella for commenting on this chapter. Thanks to Pål Puntervoll and Manuela Helmer Citterich for figures.  ...  Figure 21 . 21 12 Globplot of human CREBbinding protein (CBP_HUMAN). About half of the sequence appears to be disordered, with long flexible regions observed at the N and C termini.  ...  In this chapter we explore how these sites can be identified in proteins and describe some of the computational tools that can be used to analyze protein sequences.  ... 
doi:10.1002/3527603611.ch21 fatcat:3oar56fhrnasrgfc35dfutok4m

The C-terminal domain of the transcriptional corepressor CtBP is intrinsically unstructured

Marco Nardini, Dmitri Svergun, Peter V. Konarev, Stefania Spanò, Mauro Fasano, Chiara Bracco, Alessandra Pesce, Alessandra Donadini, Claudia Cericola, Francesco Secundo, Alberto Luini, Daniela Corda (+1 others)
2006 Protein Science  
The flexible nature of this protein region, and its structural transitions, may be instrumental for CtBP recognition and binding to diverse molecular partners.  ...  C-terminal binding proteins (CtBPs) are moonlighting proteins involved in nuclear transcriptional corepression and in Golgi membrane tubule fission.  ...  M.B. is grateful to CIMAINA (University of Milano) and to Fondazione CARIPLO (Milano, Italy) for continuous support.  ... 
doi:10.1110/ps.062115406 pmid:16597837 pmcid:PMC2242513 fatcat:5whjl2mjebe65brni5uhssho7m

Protein Disorder Prediction

Rune Linding, Lars Juhl Jensen, Francesca Diella, Peer Bork, Toby J Gibson, Robert B Russell
2003 Structure  
Biol. 315, biological function and role in neurodegenerative diseases. J. Mol. . Glob-Plot: exploring protein sequences for globularity and disorder. Nucleic Acids Res. 31, 3701-3708.  ...  We present here DisEMBL, a computational tool for prediction of disordered/unstruc-2002; Uversky, 2002). Protein disorder is important for understanding pro-tured regions within a protein sequence.  ...  Furthermore, the GlobPlot algorithm is of the definitions of disorder is most appropriate for design of protein expression vectors.  ... 
doi:10.1016/j.str.2003.10.002 pmid:14604535 fatcat:wqoqz5cvgvfnthpyw7x6varca4

Skeletal development in the sea urchin relies upon protein families that contain intrinsic disorder, aggregation-prone, and conserved globular interactive domains

Martin Pendola, Gaurav Jain, John Spencer Evans, Eugene A. Permyakov
2019 PLoS ONE  
Interestingly, three types of global conformations are predicted for the nine member protein set, wherein we note variations in the arrangement of intrinsically disordered and interactive globular domains  ...  Moreover, spicule matrix proteins possess three types of sequences: intrinsically disordered, amyloid-like, and folded protein-protein interactive.  ...  Acknowledgments This report represents contribution number 97 from the Laboratory for Chemical Physics, New York University.  ... 
doi:10.1371/journal.pone.0222068 pmid:31574084 pmcid:PMC6771980 fatcat:u72sljp5v5drfax5in3kiwm73q

Discovery of candidate KEN-box motifs using Cell Cycle keyword enrichment combined with native disorder prediction and motif conservation

Sushama Michael, Gilles Travé, Chenna Ramu, Claudia Chica, Toby J. Gibson
2008 Computer applications in the biosciences : CABIOS  
Candidates were surveyed for native disorder prediction using GlobPlot and IUPred and for motif conservation in homologues.  ...  These proteins have yet to be tested for APC/C targeted destruction, providing potential new avenues of research.  ...  G.T. was supported by EMBO and DAAD short-term fellowships. We are grateful to the anonymous referees for suggesting the mutant motif controls.  ... 
doi:10.1093/bioinformatics/btm624 pmid:18184688 fatcat:4oonfgbasng2dhk4a3j2dux6ha

Computational Methods for Protein Structure Prediction and Fold Recognition [chapter]

Iwona A. Cymerman, Marcin Feder, Marcin PawŁowski, Michal A. Kurowski, Janusz M. Bujnicki
2008 Nucleic acids and molecular biology  
The freely available on-line servers for prediction of disordered loopy regions in proteins are: NORSP (http://cubic.bioc.columbia.edu/services/NORSp/) and GLOBPLOT (http://globplot.embl.de/).  ...  On the other hand, identification of disordered, non-globular regions may help to delineate domains.  ... 
doi:10.1007/978-3-540-74268-5_1 fatcat:5tq4k56zujeorhqanga3owxbtu

Structural conservation of a short, functional, peptide-sequence motif

Susan Fox-Erlich
2009 Frontiers in Bioscience  
Krishna Kaduvera and Mr. Jay Vyas for useful discussions. This research was funded in part by US National Institutes of Health grants EB001496 and GM079689.  ...  The result is a simple graph plotting the propensity to be globular (or conversely, disordered) versus the residue number of the given protein sequence.  ...  Structural classification Globplot is a bioinformatics tool which heuristically classifies regions of any given protein sequence based on their likelihood of being natively structured (globular) or unstructured  ... 
doi:10.2741/3299 pmid:19273121 pmcid:PMC2654600 fatcat:emjzwlsmazhntlmv4sl56vocv4

Understanding eukaryotic linear motifs and their role in cell signaling and regulation

Francesca Diella
2008 Frontiers in Bioscience  
alignment; TF: transcription factor; IUP: intrinsically unstructured polypeptide; IDR: Intrinsically Disordered Regions; TM: FoldIndex.  ...  hydrophobic amino acid; NES: nuclear export signal; NPC: nuclear pore complex; SUMO: Small Ubiquitin-related Modifiers; PEP: proline-enriched tyrosine phosphatase; TCR: T-cell antigen receptor; MSA: multiple sequence  ...  ACKNOWLEDGEMENTS We thank all contributors to the ELM resource for making our work possible. This work was supported in part by the EU ProteomeBinders and EU EMBRACE (LHSG-CT-2004-512092) grants.  ... 
doi:10.2741/3175 pmid:18508681 fatcat:ccuqk353krgz7ekm36c7udeqvu

CCD 2: design constructs for protein expression, the easy way

Andrea Giovanni Murachelli, George Damaskos, Anastassis Perrakis
2021 Acta Crystallographica Section D: Structural Biology  
This information includes sequence conservation, secondary structure prediction, domain(s) and disorder detection, post-translational modifications and information on similar (domain) structures that are  ...  Studying the function or structure of proteins usually requires the generation of many protein-truncation constructs for recombinant expression, which is a tedious and error-prone job.  ...  RHPC) facility of the Netherlands Cancer Institute for hosting the CCD 2 website, and the members of the Sixma and Perrakis groups at NKI for helpful discussion, beta testing and feedback.  ... 
doi:10.1107/s2059798321005891 pmid:34342272 pmcid:PMC8329859 fatcat:2aawmrbxgff5lgi6pjadsmehou

Computational approaches to selecting and optimising targets for structural biology

Ian M. Overton, Geoffrey J. Barton
2011 Methods  
Selected targets can be optimised through construct design (e.g. to minimise protein disorder), switching to a homologous protein, and selection of experimental methodology (e.g. choice of expression system  ...  Selection of protein targets for study is central to structural biology and may be influenced by numerous factors.  ...  For example, Disembl and GlobPlot disorder are grouped together, whilst Pfam domains and RONN disorder are in a separate group.  ... 
doi:10.1016/j.ymeth.2011.08.014 pmid:21906678 pmcid:PMC3202631 fatcat:6nop3rg24zck5gjovne4spcjdu

Cluster and Fold Stability of E. coli ISC-Type Ferredoxin

Robert Yan, Salvatore Adinolfi, Clara Iannuzzi, Geoff Kelly, Alain Oregioni, Stephen Martin, Annalisa Pastore, Andrea Cavalli
2013 PLoS ONE  
NMR relaxation experiments on the cluster-loaded protein also show that, once the cluster is in place, the protein forms a globular and relatively rigid domain.  ...  The cluster-loaded protein is monomeric and well structured with a flexible C-terminus but is highly oxygen sensitive so that it readily loses the cluster leading to an irreversible unfolding under aerobic  ...  Acknowledgments We are indebted with the MRC Biomedical NMR Centre for technical support. Author Contributions  ... 
doi:10.1371/journal.pone.0078948 pmid:24265733 pmcid:PMC3827102 fatcat:jbz5iz7yhfcpdcoetaab752iuq

Page 1203 of Genetics Vol. 174, Issue 3 [page]

2006 Genetics  
Grsson, 2003b GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res. 31: 3701-3708. Locker, J., M. A. Korarski and K. D.  ...  ., 2003a Protein disorder prediction: implications for structural proteomics. Structure 11: 1453-1459. LinpInG, R., R. B. Russet, V. Nepuva and T. J.  ... 

Nuclear Magnetic Resonance Structure of the Nucleic Acid-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein 3

P. Serrano, M. A. Johnson, A. Chatterjee, B. W. Neuman, J. S. Joseph, M. J. Buchmeier, P. Kuhn, K. Wuthrich
2009 Journal of Virology  
preceding globular domain and to the following, as yet uncharacterized domain.  ...  A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns  ...  Next, two new constructs, nsp3(1066-1203) and nsp3(1066-1181), were designed based on the disordered-region prediction by GlobPlot (29) .  ... 
doi:10.1128/jvi.01253-09 pmid:19828617 pmcid:PMC2786856 fatcat:mhxophhktrea7lmfzesjvmxlny
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