What's in the BAGs? Intrinsic disorder angle of the multifunctionality of the members of a family of chaperone regulators

2021 ◽  
Author(s):  
Liberato Marzullo ◽  
Maria C. Turco ◽  
Vladimir N. Uversky
Keyword(s):  
Intrinsic Disorder

Prevalence and functionality of intrinsic disorder in human FG-nucleoporins

2021 ◽  
Vol 175 ◽  
pp. 156-170
Author(s):  
Denzelle Lee Lyngdoh ◽  
Niharika Nag ◽  
Vladimir N. Uversky ◽  
Timir Tripathi
Keyword(s):  
Intrinsic Disorder

Functional assessment of intrinsic disorder central domains of BRCA1

2015 ◽  
Vol 33 (11) ◽  
pp. 2469-2478 ◽  
Author(s):  
Lumbini R. Yadav ◽  
Sharad Rai ◽  
M.V. Hosur ◽  
Ashok K. Varma
Keyword(s):  
Functional Assessment ◽  
Intrinsic Disorder

scholarly journals On the irrationality of rational design of an HIV vaccine in light of protein intrinsic disorder

2021 ◽  
Vol 166 (5) ◽  
pp. 1283-1296
Author(s):  
Vladimir N. Uversky
Keyword(s):  
Rational Design ◽  
Intrinsic Disorder ◽  
Hiv Vaccine ◽  
Protein Intrinsic Disorder

scholarly journals Folding and Intrinsic Disorder of the Receptor Tyrosine Kinase KIT Insert Domain Seen by Conventional Molecular Dynamics Simulations

2021 ◽  
Vol 22 (14) ◽  
pp. 7375
Author(s):  
Julie Ledoux ◽  
Alain Trouvé ◽  
Luba Tchertanov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Tertiary Structure ◽  
Average Distance ◽  
Intrinsic Disorder ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Hydrophobic Core ◽  
Direct Evaluation ◽  
Dynamics Simulations

The kinase insert domain (KID) of RTK KIT is the key recruitment region for downstream signalling proteins. KID, studied by molecular dynamics simulations as a cleaved polypeptide and as a native domain fused to KIT, showed intrinsic disorder represented by a set of heterogeneous conformations. The accurate atomistic models showed that the helical fold of KID is mainly sequence dependent. However, the reduced fold of the native KID suggests that its folding is allosterically controlled by the kinase domain. The tertiary structure of KID represents a compact array of highly variable α- and 310-helices linked by flexible loops playing a principal role in the conformational diversity. The helically folded KID retains a collapsed globule-like shape due to non-covalent interactions associated in a ternary hydrophobic core. The free energy landscapes constructed from first principles—the size, the measure of the average distance between the conformations, the amount of helices and the solvent-accessible surface area—describe the KID disorder through a collection of minima (wells), providing a direct evaluation of conformational ensembles. We found that the cleaved KID simulated with restricted N- and C-ends better reproduces the native KID than the isolated polypeptide. We suggest that a cyclic, generic KID would be best suited for future studies of KID f post-transduction effects.

Intrinsic disorder in the androgen receptor: identification, characterisation and drugability

2012 ◽  
Vol 8 (1) ◽  
pp. 82-90 ◽  
Author(s):  
Iain J. McEwan
Keyword(s):  
Androgen Receptor ◽  
Intrinsic Disorder

Visualising intrinsic disorder and conformational variation in protein ensembles

2014 ◽  
Vol 169 ◽  
pp. 179-193 ◽  
Author(s):  
Julian Heinrich ◽  
Michael Krone ◽  
Seán I. O'Donoghue ◽  
Daniel Weiskopf
Keyword(s):  
Intrinsic Disorder ◽  
Molecular Graphics ◽  
Post Translational Modifications ◽  
3D Structures ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Wide Range ◽  
Conformational Variations ◽  
Protein Ensembles ◽  
Traditional Approaches

Intrinsically disordered regions (IDRs) in proteins are still not well understood, but are increasingly recognised as important in key biological functions, as well as in diseases. IDRs often confound experimental structure determination—however, they are present in many of the available 3D structures, where they exhibit a wide range of conformations, from ill-defined and highly flexible to well-defined upon binding to partner molecules, or upon post-translational modifications. Analysing such large conformational variations across ensembles of 3D structures can be complex and difficult; our goal in this paper is to improve this situation by augmenting traditional approaches (molecular graphics and principal components) with methods from human–computer interaction and information visualisation, especially parallel coordinates. We present a new tool integrating these approaches, and demonstrate how it can dissect ensembles to reveal functional insights into conformational variation and intrinsic disorder.

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