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Structural Bioinformatics Predicts Large Intrinsically Disordered Regions of Erythrocyte Binding-Like Proteins of Plasmodium sp.: Functional Implications

Arita Acharjee
2020 International Research Journal of Multidisciplinary Scope  
In this study, it is reported that EBL protein consists of massive unstructured regions in between two compact structured portions, viz., the DBD and a C-terminus trans-membrane domain as predicted from  ...  Our study reveals that its major parts of the unstructured portions consist of Intrinsically Disordered Regions (IDR).  ...  Acknowledgements The authors acknowledge IISER-Kolkata for providing research facility and International Institute of Innovation and Technology for infrastructural support. Author contribution  ... 
doi:10.47857/irjms.2020.v01i02.008 fatcat:mi2ckamcajcb7l2o6zhgqla4ru

Natively unstructured regions in proteins identified from contact predictions

Avner Schlessinger, Marco Punta, Burkhard Rost
2007 Computer applications in the biosciences : CABIOS  
Motivation: Natively unstructured (also dubbed intrinsically disordered) regions in proteins lack a defined 3D structure under physiological conditions and often adopt regular structures under particular  ...  Low propensity for the formation of internal residue contacts has been previously used to predict natively unstructured regions.  ...  This work was supported by grants from the National Library of Medicine (NLM, RO1-LM07329), by a grant from the Protein Structure Initiative of the US National Institutes of Health to the Northeast Structural  ... 
doi:10.1093/bioinformatics/btm349 pmid:17709338 fatcat:32bjhx6xc5hhtokx3tukqom7ma

Investigation of transmembrane proteins using a computational approach

Jack Y Yang, Mary Yang, A Keith Dunker, Youping Deng, Xudong Huang
2008 BMC Genomics  
to infer secondary structure from primary structure in these proteins.  ...  discriminating intrinsically unstructured segments from intrinsically structured segments in transmembrane proteins, and in using the results of these investigations to develop classifiers to identify  ...  to infer secondary structure from primary structure in these proteins.  ... 
doi:10.1186/1471-2164-9-s1-s7 pmid:18366620 pmcid:PMC2386072 fatcat:eeb3fhvepraihmfsc52w4oliy4

Intrinsically Unstructured Proteins: Potential Targets for Drug Discovery

Pathan Salma, Chintan Chhatbar, Sriram Seshadri
2009 American Journal of Infectious Diseases  
Approach: A significant number of proteins known to be involved in protein deposition disorders were now considered to Be Intrinsically Unstructured Proteins (IUPs).  ...  Obviously, IUP's were greatly underrepresented in the Protein Data Bank, although there were few cases of an IUP bound to a folded (intrinsically structured) protein.  ...  regions of the molecule are unstructured [50] .  ... 
doi:10.3844/ajidsp.2009.133.141 fatcat:rxswi6r6vvckhkorpwsm4mu7ui

Intrinsically Unstructured Proteins: Potential Targets for Drug Discovery

Salma
2009 American Journal of Infectious Diseases  
Approach: A significant number of proteins known to be involved in protein deposition disorders were now considered to Be Intrinsically Unstructured Proteins (IUPs).  ...  Obviously, IUP's were greatly underrepresented in the Protein Data Bank, although there were few cases of an IUP bound to a folded (intrinsically structured) protein.  ...  regions of the molecule are unstructured [50] .  ... 
doi:10.3844/ajidsp.2009.126.134 fatcat:2bldgq3fx5efplqwa5tecmz3ha

Prediction and Experimental Detection of Structural and Functional Motifs in Intrinsically Unfolded Proteins [chapter]

Cesira de, Annalisa Pastore
2011 Selected Works in Bioinformatics  
Introduction Intrinsically unstructured proteins (IUPs) or proteins with intrinsically unstructured regions (IURs) have quickly gained increasing interest within the biological community because of their  ...  The terms IUPs and IURs designate proteins or protein regions intrinsically devoid of a well defined tertiary structure.  ...  Prediction and Experimental Detection of Structural and Functional Motifs in Intrinsically Unfolded Proteins, Selected Works in Bioinformatics, Dr.  ... 
doi:10.5772/23168 fatcat:qcymlftlkzeztd4qk7sgfbkjyy

Structural analysis of human respiratory syncytial virus P protein: identification of intrinsically disordered domains

Fernando M Simabuco, John M Asara, Manuel C Guerrero, Towia A Libermann, Luiz F Zerbini, Armando M Ventura
2011 Brazilian Journal of Microbiology  
In this report we describe that HRSV P protein has putative intrinsically disordered domains predicted by in silico methods.  ...  Disordered domains can play a role in protein interaction, and the present data contribute to the comprehension of HRSV P protein interactions in the viral replication complex.  ...  ACKNOWLEDGEMENTS for protein chromatography support. All the content of the journal, except where otherwise noted, is licensed under a Creative Commons License  ... 
doi:10.1590/s1517-83822011000100043 pmid:24031640 pmcid:PMC3768923 fatcat:6oibu3id4neonatiakruvcmd6q

The Orderly Chaos of Proteins

A. Keith Dunker, Richard W. Kriwacki
2011 Scientific American  
Thus, calcineurin is like two proteins in one: the structured region performs catalysis, and the unstructured region regulates this catalytic function.  ...  The kinases themselves fall near the opposite end of this scale. Many other proteins lie somewhere in between, having both structured and unstructured regions.  ... 
doi:10.1038/scientificamerican0411-68 fatcat:n2tiqc5jezcg5lvnxnzzbrg4hu

Proteins special issue of biopolymers

Alfred Wittinghofer, Jean Baum Martin, Stephen Blacklow
2013 Biopolymers  
ALFRED WITTINGHOFER Department of Structural Biology Max-Planck-Institute for Molecular Physiology Dortmund, Germany  ...  A large number of proteins, possibly up to 30%, are intrinsically unfolded or contain, in addition to folded domains, intrinsically unstructured regions.  ...  Unstructured proteins or regions play many roles in biology, but are also contributory to disease pathogenesis.  ... 
doi:10.1002/bip.22353 pmid:23893350 fatcat:fp45zmm47rhbtkqinr4fx5q5um

Microstructuralism and macromolecules: the case of moonlighting proteins

Emma Tobin
2009 Foundations of Chemistry: Philosophical, Historical, Educational and Interdisciplinary Studies of Chemistry  
In this paper, several microstructural theses are distinguished. An analysis of macromolecules such as moonlighting proteins suggests that all the forms of microstructuralism cannot accommodate them.  ...  Microstructuralism in the philosophy of chemistry is the thesis that chemical kinds can be individuated in terms of their microstructural properties (Hendry in Philos Sci 73: [864][865][866][867][868][  ...  I also wish to acknowledge the AHRC for financially supporting a period of postdoctoral research, as a core researcher on the metaphysics of science project, during which this paper was written.  ... 
doi:10.1007/s10698-009-9078-5 fatcat:njia2i5aird5nhmlc5x74ctim4

Phosphoproteomic Analysis of the Mouse Brain Cytosol Reveals a Predominance of Protein Phosphorylation in Regions of Intrinsic Sequence Disorder

Mark O. Collins, Lu Yu, Iain Campuzano, Seth G. N. Grant, Jyoti S. Choudhary
2008 Molecular & Cellular Proteomics  
The majority of phosphorylation sites found by MS were located outside of structural protein domains (97%) but were mostly located in regions of intrinsic sequence disorder (86%). 368 phosphorylation sites  ...  In addition, we found that 58 phosphorylation sites in this data set occur in 14-3-3 binding consensus motifs, linear motifs that are associated with unstructured regions in proteins.  ...  It has been suggested that intrinsic sequence disorder, which is specified by primary sequence composition and manifests itself as flexible or unstructured regions in proteins, is associated with protein  ... 
doi:10.1074/mcp.m700564-mcp200 pmid:18388127 fatcat:trswgvwgkre4fam77oixo2vu6u

Deciphering Mode of Action of Functionally Important Regions in the Intrinsically Disordered Paxillin (Residues 1-313) Using Its Interaction with FAT (Focal Adhesion Targeting Domain of Focal Adhesion Kinase)

Muniasamy Neerathilingam, Sneha G. Bairy, Sumukh Mysore, L. Michel Espinoza-Fonseca
2016 PLoS ONE  
Therefore, using simple and swift strategies for identifying functionally important regions in unstructured segments and understanding their underlying mechanisms is critical for many applications.  ...  Intrinsically disordered proteins (IDPs) play a major role in various cellular functions ranging from transcription to cell migration.  ...  Hoellerer for providing the GST-FAT and other LD peptides used in the study. We would like to thank Ambika Doddamani for preparation of constructs required for the Bio-layer Interferometry studies.  ... 
doi:10.1371/journal.pone.0150153 pmid:26928467 pmcid:PMC4771712 fatcat:wcuff3yp7bchznx7g6otbir47y

Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicle

Silvia Vilasi, Raffaele Ragone
2008 The FEBS Journal  
of intrinsically unfolded and ideally globular proteins.  ...  It was inferred that the global structure of SV-IV is not similar to any protein of known three-dimensional structure.  ...  Betraying still imperfect categorization, these systems are currently classified as 'intrinsically disordered proteins' (IDPs), but the use of other synonymous expressions, such 'as intrinsically unstructured  ... 
doi:10.1111/j.1742-4658.2007.06242.x pmid:18215165 fatcat:ylc3kupghrccnlzlncxnbzrzgq

Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicle

Silvia Vilasi, Raffaele Ragone
2007 Nature Precedings  
of intrinsically unfolded and ideally globular proteins.  ...  It was inferred that the global structure of SV-IV is not similar to any protein of known three-dimensional structure.  ...  Betraying still imperfect categorization, these systems are currently classified as 'intrinsically disordered proteins' (IDPs), but the use of other synonymous expressions, such 'as intrinsically unstructured  ... 
doi:10.1038/npre.2007.1394.1 fatcat:yjrlypfv5fd2bfwaoutadmqale

Prediction of unfolded segments in a protein sequence based on amino acid composition

K. Coeytaux, A. Poupon
2005 Bioinformatics  
Using this distribution, we calculate for a given sequence fragment the probability to be part of either a structured or an unstructured region.  ...  This intrinsic disorder is related to certain critical functions. Apart from their fundamental interest, unstructured regions in proteins may prevent crystallization.  ...  ACKNOWLEDGEMENTS We thank Herman van Tilbeurgh and Michael Levitt for helpful discussions and for critical reading of the manuscript. This work was  ... 
doi:10.1093/bioinformatics/bti266 pmid:15657106 fatcat:inlbmn525rcxjk7ten5u6ccbfa
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