scholarly journals Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications

2015 ◽  
Vol 3 ◽  
Author(s):  
Karl J. Niklas ◽  
Sarah E. Bondos ◽  
A. Keith Dunker ◽  
Stuart A. Newman
Keyword(s):  
Alternative Splicing ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Protein Domains ◽  
Intrinsically Disordered Protein ◽  
Post Translational Modifications ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Gene Regulatory

scholarly journals PhosIDP: a web tool to visualize the location of phosphorylation sites in disordered regions

2021 ◽  
Author(s):  
Sonia T. Nicolaou ◽  
Max Hebditch ◽  
Owen J. Jonathan ◽  
Chandra S. Verma ◽  
Jim Warwicker
Keyword(s):  
Protein Domains ◽  
Intrinsically Disordered Protein ◽  
Phosphorylation Sites ◽  
Web Tool ◽  
Functional Interpretation ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Intrinsically Disordered Region ◽  
Condensate Formation ◽  
The Web

AbstractCharge is a key determinant of intrinsically disordered protein (IDP) and intrinsically disordered region (IDR) properties. IDPs and IDRs are enriched in sites of phosphorylation, which alters charge. Visualizing the degree to which phosphorylation modulates the charge profile of a sequence would assist in the functional interpretation of IDPs and IDRs. PhosIDP is a web tool that shows variation of charge and fold propensity upon phosphorylation. In combination with the displayed location of protein domains, the information provided by the web tool can lead to functional inferences for the consequences of phosphorylation. IDRs are components of many proteins that form biological condensates. It is shown that IDR charge, and its modulation by phosphorylation, is more tightly controlled for proteins that are essential for condensate formation than for those present in condensates but inessential.

scholarly journals Phosphorylation regulates the binding of intrinsically disordered proteins via a flexible conformation selection mechanism

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Na Liu ◽  
Yue Guo ◽  
Shangbo Ning ◽  
Mojie Duan
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Hydrophobic Interactions ◽  
Intrinsically Disordered Protein ◽  
Disordered Proteins ◽  
Regulation Mechanism ◽  
Enhanced Sampling ◽  
Dynamic Interactions ◽  
Post Translational Modifications ◽  
Intrinsically Disordered ◽  
Disordered Protein

Abstract Phosphorylation is one of the most common post-translational modifications. The phosphorylation of the kinase-inducible domain (KID), which is an intrinsically disordered protein (IDP), promotes the folding of KID and binding with the KID-interacting domain (KIX). However, the regulation mechanism of the phosphorylation on KID is still elusive. In this study, the structural ensembles and binding process of pKID and KIX are studied by all-atom enhanced sampling technologies. The results show that more hydrophobic interactions are formed in pKID, which promote the formation of the special hydrophobic residue cluster (HRC). The pre-formed HRC promotes binding to the correct sites of KIX and further lead the folding of pKID. Consequently, a flexible conformational selection model is proposed to describe the binding and folding process of intrinsically disordered proteins. The binding mechanism revealed in this work provides new insights into the dynamic interactions and phosphorylation regulation of proteins.

scholarly journals Fast Association and Slow Transitions in the Interaction between Two Intrinsically Disordered Protein Domains

2012 ◽  
Vol 287 (41) ◽  
pp. 34316-34324 ◽  
Author(s):  
Jakob Dogan ◽  
Tanja Schmidt ◽  
Xin Mu ◽  
Åke Engström ◽  
Per Jemth
Keyword(s):  
Protein Domains ◽  
Intrinsically Disordered Protein ◽  
Intrinsically Disordered ◽  
Disordered Protein

Acceleration of an Enzymatic Reaction in Liquid Phase Separated Compartments Based on Intrinsically Disordered Protein Domains

2020 ◽  
Vol 2 (4) ◽  
Author(s):  
Andreas M. Küffner ◽  
Marc Prodan ◽  
Remo Zuccarini ◽  
Umberto Capasso Palmiero ◽  
Lenka Faltova ◽  
...  
Keyword(s):  
Liquid Phase ◽  
Enzymatic Reaction ◽  
Protein Domains ◽  
Intrinsically Disordered Protein ◽  
Intrinsically Disordered ◽  
Disordered Protein
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