PMID- 27881680
OWN - NLM
STAT- MEDLINE
DCOM- 20170601
LR  - 20210205
IS  - 1083-351X (Electronic)
IS  - 0021-9258 (Print)
IS  - 0021-9258 (Linking)
VI  - 292
IP  - 2
DP  - 2017 Jan 13
TI  - Structures and Short Linear Motif of Disordered Transcription Factor Regions 
      Provide Clues to the Interactome of the Cellular Hub Protein Radical-induced Cell 
      Death1.
PG  - 512-527
LID - 10.1074/jbc.M116.753426 [doi]
AB  - Intrinsically disordered protein regions (IDRs) lack a well defined 
      three-dimensional structure but often facilitate key protein functions. Some 
      interactions between IDRs and folded protein domains rely on short linear motifs 
      (SLiMs). These motifs are challenging to identify, but once found they can point 
      to larger networks of interactions, such as with proteins that serve as hubs for 
      essential cellular functions. The stress-associated plant protein radical-induced 
      cell death1 (RCD1) is one such hub, interacting with many transcription factors 
      via their flexible IDRs. To identify the SLiM bound by RCD1, we analyzed the IDRs 
      in three protein partners, DREB2A (dehydration-responsive element-binding protein 
      2A), ANAC013, and ANAC046, considering parameters such as disorder, context, 
      charges, and pI. Using a combined bioinformatics and experimental approach, we 
      have identified the bipartite RCD1-binding SLiM as (DE)X(1,2)(YF)X(1,4)(DE)L, 
      with essential contributions from conserved aromatic, acidic, and leucine 
      residues. Detailed thermodynamic analysis revealed both favorable and unfavorable 
      contributions from the IDRs surrounding the SLiM to the interactions with RCD1, 
      and the SLiM affinities ranged from low nanomolar to 50 times higher K(d) values. 
      Specifically, although the SLiM was surrounded by IDRs, individual intrinsic 
      alpha-helix propensities varied as shown by CD spectroscopy. NMR spectroscopy further 
      demonstrated that DREB2A underwent coupled folding and binding with alpha-helix 
      formation upon interaction with RCD1, whereas peptides from ANAC013 and ANAC046 
      formed different structures or were fuzzy in the complexes. These findings allow 
      us to present a model of the stress-associated RCD1-transcription factor 
      interactome and to contribute to the emerging understanding of the interactions 
      between folded hubs and their intrinsically disordered partners.
CI  - (c) 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
FAU - O'Shea, Charlotte
AU  - O'Shea C
AD  - From the Linderstrom-Lang Centre for Protein Science, Department of Biology, 
      University of Copenhagen, 5 Ole Maaloes Vej, Copenhagen DK-2200, Denmark.
FAU - Staby, Lasse
AU  - Staby L
AD  - From the Linderstrom-Lang Centre for Protein Science, Department of Biology, 
      University of Copenhagen, 5 Ole Maaloes Vej, Copenhagen DK-2200, Denmark.
FAU - Bendsen, Sidsel Krogh
AU  - Bendsen SK
AD  - From the Linderstrom-Lang Centre for Protein Science, Department of Biology, 
      University of Copenhagen, 5 Ole Maaloes Vej, Copenhagen DK-2200, Denmark.
FAU - Tidemand, Frederik Gronbaek
AU  - Tidemand FG
AD  - From the Linderstrom-Lang Centre for Protein Science, Department of Biology, 
      University of Copenhagen, 5 Ole Maaloes Vej, Copenhagen DK-2200, Denmark.
FAU - Redsted, Andreas
AU  - Redsted A
AD  - From the Linderstrom-Lang Centre for Protein Science, Department of Biology, 
      University of Copenhagen, 5 Ole Maaloes Vej, Copenhagen DK-2200, Denmark.
FAU - Willemoes, Martin
AU  - Willemoes M
AD  - From the Linderstrom-Lang Centre for Protein Science, Department of Biology, 
      University of Copenhagen, 5 Ole Maaloes Vej, Copenhagen DK-2200, Denmark.
FAU - Kragelund, Birthe B
AU  - Kragelund BB
AD  - From the Linderstrom-Lang Centre for Protein Science, Department of Biology, 
      University of Copenhagen, 5 Ole Maaloes Vej, Copenhagen DK-2200, Denmark.
FAU - Skriver, Karen
AU  - Skriver K
AD  - From the Linderstrom-Lang Centre for Protein Science, Department of Biology, 
      University of Copenhagen, 5 Ole Maaloes Vej, Copenhagen DK-2200, Denmark 
      kskriver@bio.ku.dk.
LA  - eng
PT  - Journal Article
DEP - 20161123
PL  - United States
TA  - J Biol Chem
JT  - The Journal of biological chemistry
JID - 2985121R
RN  - 0 (ANAC013 protein, Arabidopsis)
RN  - 0 (Arabidopsis Proteins)
RN  - 0 (DREB2A protein, Arabidopsis)
RN  - 0 (Nuclear Proteins)
RN  - 0 (RCD1 protein, Arabidopsis)
RN  - 0 (Transcription Factors)
SB  - IM
MH  - Amino Acid Motifs
MH  - Arabidopsis/*chemistry/genetics/metabolism
MH  - Arabidopsis Proteins/*chemistry/genetics/metabolism
MH  - *Models, Molecular
MH  - Nuclear Magnetic Resonance, Biomolecular
MH  - Nuclear Proteins/*chemistry/genetics/metabolism
MH  - Protein Binding
MH  - *Protein Folding
MH  - Transcription Factors/*chemistry/genetics/metabolism
PMC - PMC5241728
OTO - NOTNLM
OT  - Arabidopsis thaliana
OT  - SLiM
OT  - affinity
OT  - coupled folding and binding
OT  - interactome
OT  - intrinsically disordered protein
OT  - nuclear magnetic resonance (NMR)
OT  - plant stress
OT  - protein-protein interaction
OT  - thermodynamics
EDAT- 2016/11/25 06:00
MHDA- 2017/06/02 06:00
PMCR- 2018/01/13
CRDT- 2016/11/25 06:00
PHST- 2016/08/12 00:00 [received]
PHST- 2016/11/23 00:00 [revised]
PHST- 2016/11/25 06:00 [pubmed]
PHST- 2017/06/02 06:00 [medline]
PHST- 2016/11/25 06:00 [entrez]
PHST- 2018/01/13 00:00 [pmc-release]
AID - S0021-9258(20)40184-X [pii]
AID - M116.753426 [pii]
AID - 10.1074/jbc.M116.753426 [doi]
PST - ppublish
SO  - J Biol Chem. 2017 Jan 13;292(2):512-527. doi: 10.1074/jbc.M116.753426. Epub 2016 
      Nov 23.