PMID- 27028374
OWN - NLM
STAT- MEDLINE
DCOM- 20170621
LR  - 20171117
IS  - 1742-4658 (Electronic)
IS  - 1742-464X (Linking)
VI  - 283
IP  - 12
DP  - 2016 Jun
TI  - The red edge excitation shift phenomenon can be used to unmask protein structural 
      ensembles: implications for NEMO-ubiquitin interactions.
PG  - 2272-84
LID - 10.1111/febs.13724 [doi]
AB  - To understand complex molecular interactions, it is necessary to account for 
      molecular flexibility and the available equilibrium of conformational states. 
      Only a small number of experimental approaches can access such information. 
      Potentially steady-state red edge excitation shift (REES) spectroscopy can act as 
      a qualitative metric of changes to the protein free energy landscape (FEL) and 
      the equilibrium of conformational states. First, we validate this hypothesis 
      using a single Trp-containing protein, NF-kappaB essential modulator (NEMO). We 
      provide detailed evidence from chemical denaturation studies, macromolecular 
      crowding studies, and the first report of the pressure dependence of the REES 
      effect. Combination of these data demonstrate that the REES effect can report on 
      the 'ruggedness' of the FEL and we present a phenomenological model, based on 
      realistic physical interpretations, for fitting steady-state REES data to allow 
      quantification of this aspect of the REES effect. We test the conceptual 
      framework we have developed by correlating findings from NEMO ligand-binding 
      studies with the REES data in a range of NEMO-ligand binary complexes. Our 
      findings shed light on the nature of the interaction between NEMO and 
      poly-ubiquitin, suggesting that NEMO is differentially regulated by 
      poly-ubiquitin chain length and that this regulation occurs via a modulation of 
      the available equilibrium of conformational states, rather than gross structural 
      change. This study therefore demonstrates the potential of REES as a powerful 
      tool for tackling contemporary issues in structural biology and biophysics and 
      elucidates novel information on the structure-function relationship of NEMO and 
      key interaction partners.
CI  - (c) 2016 Federation of European Biochemical Societies.
FAU - Catici, Dragana A M
AU  - Catici DA
AD  - Department of Biology and Biochemistry, Faculty of Science, University of Bath, 
      UK.
FAU - Amos, Hope E
AU  - Amos HE
AD  - Department of Biology and Biochemistry, Faculty of Science, University of Bath, 
      UK.
FAU - Yang, Yi
AU  - Yang Y
AD  - Department of Biology and Biochemistry, Faculty of Science, University of Bath, 
      UK.
FAU - van den Elsen, Jean M H
AU  - van den Elsen JM
AD  - Department of Biology and Biochemistry, Faculty of Science, University of Bath, 
      UK.
FAU - Pudney, Christopher R
AU  - Pudney CR
AD  - Department of Biology and Biochemistry, Faculty of Science, University of Bath, 
      UK.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20160609
PL  - England
TA  - FEBS J
JT  - The FEBS journal
JID - 101229646
RN  - 0 (IKBKG protein, human)
RN  - 0 (Ligands)
RN  - 0 (NF-kappa B)
RN  - 120904-94-1 (Polyubiquitin)
RN  - EC 2.7.11.10 (I-kappa B Kinase)
SB  - IM
MH  - Binding Sites
MH  - I-kappa B Kinase/*chemistry/genetics
MH  - Ligands
MH  - NF-kappa B/*chemistry/genetics
MH  - Polyubiquitin/*chemistry/genetics
MH  - Protein Binding
MH  - *Protein Conformation
MH  - Spectrometry, Fluorescence
OTO - NOTNLM
OT  - NEMO
OT  - free energy landscape
OT  - protein dynamics
OT  - red edge excitation shift
OT  - tryptophan fluorescence
EDAT- 2016/03/31 06:00
MHDA- 2017/06/22 06:00
CRDT- 2016/03/31 06:00
PHST- 2016/03/11 00:00 [received]
PHST- 2016/03/29 00:00 [accepted]
PHST- 2016/03/31 06:00 [entrez]
PHST- 2016/03/31 06:00 [pubmed]
PHST- 2017/06/22 06:00 [medline]
AID - 10.1111/febs.13724 [doi]
PST - ppublish
SO  - FEBS J. 2016 Jun;283(12):2272-84. doi: 10.1111/febs.13724. Epub 2016 Jun 9.