bHLH–PAS Proteins: Their Structure and Intrinsic Disorder
Abstract
:1. Introduction to bHLH–PAS Proteins
2. bHLH–PAS Protein Conservation between Organisms
3. Structure of bHLH–PAS Proteins
4. Unique Properties of the C-Terminal Domains of bHLH–PAS Proteins as IDRs
4.1. In Silico Analyses of Selected bHLH–PAS Proteins
4.2. The Impact of Disordered Regions on Protein Function
4.3. Structural Analysis of bHLH–PAS C-Terminal Fragments
4.4. Structural Analysis of IDPs
5. Conclusions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
Aa | amino acid |
AHR | aryl hydrocarbon receptor |
AHRR | aryl hydrocarbon receptor repressor |
ARNT | aryl hydrocarbon receptor nuclear translocator |
bHLH–PAS | helix–loop–helix/Per-ARNT-SIM |
CLOCK | circadian locomotor output cycles protein kaput |
CRY1 | cryptochrome |
DYS | dysfusion protein |
ER | estrogen receptor |
GCE | germ cell-expressed protein |
HAT | histone transacetylase |
HIF | hypoxia-inducible factors |
IDPs | intrinsically disordered proteins |
IDRs | intrinsically disordered regions |
JH | juvenile hormone |
LBD | ligand-binding domain |
MET | methoprene-tolerant protein |
MoREs | molecular recognition elements |
MET/C | C-terminus of the MET protein |
NES | nuclear export signal |
NLS | nuclear localization signal |
NMR | Nuclear Resonance Magnetism |
NPAS | neuronal PAS domain-containing proteins |
NR | boxes nuclear receptor boxes |
PAC | PAS-associated C-terminal motif |
PDB | Protein Data Bank |
PREs | paramagnetic relaxation enhancements |
RDCs | residual dipolar couplings |
SAXS | Small-angle X-ray Scattering |
SIM | single-minded proteins |
SIMA | similar protein |
SS | spineless protein |
TAD or TRD | transactivation or repression domain |
TGO | TANGO protein |
TRH | trachealess protein |
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Class I | Class II | Type of Signal |
---|---|---|
hypoxia-inducible factors (HIF; HIF1-α, HIF2-α, and HIF3-α) | aryl hydrocarbon receptor nuclear translocator (ARNT), also known as HIF1-β and ARNT2 | regulated by hypoxia |
aryl hydrocarbon receptor (AHR); aryl hydrocarbon receptor repressor (AHRR) | regulated by xenobiotics | |
single-minded proteins (SIM1 and SIM2) | developmentally regulated | |
neuronal PAS domain proteins (NPAS) | developmentally regulated | |
circadian locomotor output cycles protein kaput (CLOCK) | Circadian rhythm proteins (BMAL1 and BMAL2, also known as ARNTL and ARNTL2) | circadian rhythms |
Form | Protein | Segment | Organism | PDB ID |
---|---|---|---|---|
monomers | HIF2-α | PAS-B domain | Homo sapiens | 1P97 |
ARNT | PAS-B domain | Homo sapiens | 1X0O | |
dimer | HIF-2a:ARNT | PAS-B domains | Homo sapiens | 2A24 |
Form | Protein | Segment | Organism | PDB ID |
---|---|---|---|---|
monomers | AHR | PAS-A | Mus musculus | 4M4X |
ARNT | PAS-B | Homo sapiens | 2B02 | |
HIF1-α | PAS-B | Homo sapiens | 4H6J | |
dimers | ARNT Homodimer | PAS-B | Homo sapiens | 4EQ1 |
HIF2-α:ARNT | PAS-B | Homo sapiens | 3F1P | |
HIF2-α:ARNT with artificial ligand | PAS-B | Homo sapiens | 3F1O | |
HIF2-α:ARNT | PAS-B | Homo sapiens | 6D0C | |
ARNT/HIF transcription factor/coactivator complex | PAS-B | Homo sapiens, Mus musculus | 4PKY | |
ARNT transcription factor/coactivator complex | PAS-B domain | Homo sapiens, Mus musculus | 4LPZ | |
HIF2-α:ARNT | bHLH; PAS-A; PAS-B | Mus musculus | 4ZP4 | |
HIF2-α:ARNT with HRE DNA | bHLH; PAS-A; PAS-B | Mus musculus | 4ZPK | |
HIF1-α:ARNT with HRE DNA | bHLH; PAS-A; PAS-B | Mus musculus | 4ZPR | |
AHR:ARNT | bHLH; PAS-A | Homo sapiens | 5NJ8 | |
AHR:ARNT bound to the dioxin response element (DRE) | bHLH; PAS-A | Homo sapiens, Mus musculus | 5V0L | |
AHRR:ARNT | bHLH; PAS-A; PAS-B | Homo sapiens, Bos taurus | 5Y7Y | |
NPAS1:ARNT | bHLH; PAS-A; PAS-B | Mus musculus | 5SY5 | |
NPAS3:ARNT in complex with HRE DNA | bHLH; PAS-A; PAS-B | Mus musculus | 5SY7 | |
CLOCK-BMAL1 | bHLH | Homo sapiens | 4H10 | |
CLOCK:BMAL1 | bHLH; PAS-A; PAS-B | Mus musculus | 4F3L |
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Kolonko, M.; Greb-Markiewicz, B. bHLH–PAS Proteins: Their Structure and Intrinsic Disorder. Int. J. Mol. Sci. 2019, 20, 3653. https://doi.org/10.3390/ijms20153653
Kolonko M, Greb-Markiewicz B. bHLH–PAS Proteins: Their Structure and Intrinsic Disorder. International Journal of Molecular Sciences. 2019; 20(15):3653. https://doi.org/10.3390/ijms20153653
Chicago/Turabian StyleKolonko, Marta, and Beata Greb-Markiewicz. 2019. "bHLH–PAS Proteins: Their Structure and Intrinsic Disorder" International Journal of Molecular Sciences 20, no. 15: 3653. https://doi.org/10.3390/ijms20153653