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Journal articles on the topic 'Per Arnt Sim (PAS)'

Author: Grafiati

Published: 10 December 2022

Last updated: 31 July 2025

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1

Yang, Jinsong, Lei Zhang, Paul J. A. Erbel, et al. "Functions of the Per/ARNT/Sim Domains of the Hypoxia-inducible Factor." Journal of Biological Chemistry 280, no. 43 (2005): 36047–54. http://dx.doi.org/10.1074/jbc.m501755200.

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The heterodimeric transcription factor hypoxia-inducible factor (HIF) plays an important role in the progression of a number of processes in which O2 availability is compromised and, as such, has become an increasingly attractive therapeutic target. Although tremendous progress has been made in recent years in unraveling the mechanisms underlying O2-dependent regulation of HIF through its O2-dependent degradation domain and C-terminal transactivation domain, our understanding of the contributions of other structural elements, particularly the Per/ARNT/Sim (PAS)-A and PAS-B domains, to the acti

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2

Hirose, K., M. Morita, M. Ema, et al. "cDNA cloning and tissue-specific expression of a novel basic helix-loop-helix/PAS factor (Arnt2) with close sequence similarity to the aryl hydrocarbon receptor nuclear translocator (Arnt)." Molecular and Cellular Biology 16, no. 4 (1996): 1706–13. http://dx.doi.org/10.1128/mcb.16.4.1706.

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We isolated mouse cDNA clones (Arnt2) that are highly similar to but distinct from the aryl hydrocarbon receptor (AhR) nuclear translocator (Arnt). The composite cDNA covered a 2,443-bp sequence consisting of a putative 2,136-bp open reading frame encoding a polypeptide of 712 amino acids. The predicted Arnt2 polypeptide carries a characteristic basic helix-loop-helix (bHLH)/PAS motif in its N-terminal region with close similarity (81% identity) to that of mouse Arnt and has an overall sequence identity of 57% with Arnt. Biochemical properties and interaction of Arnt2 with other bHLH/PAS prote

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3

Reisz-Porszasz, S., M. R. Probst, B. N. Fukunaga, and O. Hankinson. "Identification of functional domains of the aryl hydrocarbon receptor nuclear translocator protein (ARNT)." Molecular and Cellular Biology 14, no. 9 (1994): 6075–86. http://dx.doi.org/10.1128/mcb.14.9.6075-6086.1994.

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The activated aryl hydrocarbon receptor (AHR) and the AHR nuclear translocator (ARNT) bind DNA as a heterodimer. Both proteins represent a novel class of basic helix-loop-helix (bHLH)-containing transcription factors in that (i) activation of AHR requires the binding of ligand (e.g., 2,3,7,8-tetrachlorodibenzo-p-dioxin [TCDD]), (ii) the xenobiotic responsive element (XRE) recognized by the AHR/ARNT heterodimer differs from the recognition sequence for nearly all other bHLH proteins, and (iii) both proteins contain a PAS homology region, which in the Drosophila PER and SIM proteins functions as

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4

Reisz-Porszasz, S., M. R. Probst, B. N. Fukunaga, and O. Hankinson. "Identification of functional domains of the aryl hydrocarbon receptor nuclear translocator protein (ARNT)." Molecular and Cellular Biology 14, no. 9 (1994): 6075–86. http://dx.doi.org/10.1128/mcb.14.9.6075.

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The activated aryl hydrocarbon receptor (AHR) and the AHR nuclear translocator (ARNT) bind DNA as a heterodimer. Both proteins represent a novel class of basic helix-loop-helix (bHLH)-containing transcription factors in that (i) activation of AHR requires the binding of ligand (e.g., 2,3,7,8-tetrachlorodibenzo-p-dioxin [TCDD]), (ii) the xenobiotic responsive element (XRE) recognized by the AHR/ARNT heterodimer differs from the recognition sequence for nearly all other bHLH proteins, and (iii) both proteins contain a PAS homology region, which in the Drosophila PER and SIM proteins functions as

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5

Wang, Feng, Shengli Shi, Ruixue Zhang, and Oliver Hankinson. "Identifying target genes of the aryl hydrocarbon receptor nuclear translocator (Arnt) using DNA microarray analysis." Biological Chemistry 387, no. 9 (2006): 1215–18. http://dx.doi.org/10.1515/bc.2006.150.

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Abstract The aryl hydrocarbon receptor nuclear translocator (Arnt) is a basic helix-loop-helix (bHLH) protein that also contains a Per-Arnt-Sim (PAS) domain. In addition to forming heterodimers with many other bHLH-PAS proteins, including the aryl hydrocarbon receptor (AhR) and hypoxia-inducible factors 1α, 2α and 3α, Arnt can also form homodimers when expressed from its cDNA in vitro or in vivo. However, target genes of the Arnt/Arnt homodimer remain to be identified. In this study, we have elucidated the profile of genes responsive to the reintroduction of Arnt expression in an Arnt-deficien

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6

de Souza, João V., Sylvia Reznikov, Ruidi Zhu, and Agnieszka K. Bronowska. "Druggability assessment of mammalian Per–Arnt–Sim [PAS] domains using computational approaches." MedChemComm 10, no. 7 (2019): 1126–37. http://dx.doi.org/10.1039/c9md00148d.

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7

Moffett, P., M. Reece, and J. Pelletier. "The murine Sim-2 gene product inhibits transcription by active repression and functional interference." Molecular and Cellular Biology 17, no. 9 (1997): 4933–47. http://dx.doi.org/10.1128/mcb.17.9.4933.

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The Drosophila single-minded (Dsim) gene encodes a master regulatory protein involved in cell fate determination during midline development. This protein is a member of a rapidly expanding family of gene products possessing basic helix-loop-helix (bHLH) and hydrophobic PAS (designated a conserved region among PER, ARNT [aryl hydrocarbon receptor nuclear translocator] and SIM) protein association domains. Members of this family function as central transcriptional regulators in cellular differentiation and in the response to environmental stimuli such as xenobiotics and hypoxia. We have previous

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8

Pongratz, Ingemar, Camilla Antonsson, Murray L. Whitelaw, and Lorenz Poellinger. "Role of the PAS Domain in Regulation of Dimerization and DNA Binding Specificity of the Dioxin Receptor." Molecular and Cellular Biology 18, no. 7 (1998): 4079–88. http://dx.doi.org/10.1128/mcb.18.7.4079.

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ABSTRACT The dioxin receptor is a ligand-regulated transcription factor that mediates signal transduction by dioxin and related environmental pollutants. The receptor belongs to the basic helix-loop-helix (bHLH)–Per-Arnt-Sim (PAS) family of factors, which, in addition to the bHLH motif, contain a PAS region of homology. Upon activation, the dioxin receptor dimerizes with the bHLH-PAS factor Arnt, enabling the receptor to recognize xenobiotic response elements in the vicinity of target genes. We have studied the role of the PAS domain in dimerization and DNA binding specificity of the dioxin re

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9

Zhao, J. M., H. Lee, R. A. Nome, S. Majid, N. F. Scherer, and W. D. Hoff. "Single-molecule detection of structural changes during Per-Arnt-Sim (PAS) domain activation." Proceedings of the National Academy of Sciences 103, no. 31 (2006): 11561–66. http://dx.doi.org/10.1073/pnas.0601567103.

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10

MacDonald, P. E., and P. Rorsman. "Per-arnt-sim (PAS) domain kinase (PASK) as a regulator of glucagon secretion." Diabetologia 54, no. 4 (2011): 719–21. http://dx.doi.org/10.1007/s00125-011-2072-1.

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11

Adaixo, Ricardo, and João Henrique Morais-Cabral. "Crystallization and preliminary crystallographic characterization of the PAS domains of EAG and ELK potassium channels." Acta Crystallographica Section F Structural Biology and Crystallization Communications 66, no. 9 (2010): 1056–59. http://dx.doi.org/10.1107/s1744309110027880.

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Per–Arnt–Sim (PAS) domains are ubiquitous in nature; they are ∼130-amino-acid protein domains that adopt a fairly conserved three-dimensional structure despite their low degree of sequence homology. These domains constitute the N-terminus or, less frequently, the C-terminus of a number of proteins, where they exert regulatory functions. PAS-containing proteins generally display two or more copies of this motif. In this work, the crystallization and preliminary analysis of the PAS domains of two eukaryotic potassium channels from the ether-à-go-go (EAG) family are reported.

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12

Philip, A. F., M. Kumauchi, and W. D. Hoff. "Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain." Proceedings of the National Academy of Sciences 107, no. 42 (2010): 17986–91. http://dx.doi.org/10.1073/pnas.1004823107.

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13

de Souza, João Victor, Piotr Zaborniak, Sylvia Reznikov, Matthew Kondal, Ruidi Zhu, and Agnieszka K. Bronowska. "Molecular Forces Governing the Biological Function of Per-Arnt-Sim-B (PAS-B) Domains: A Comparative Computational Study." Biophysica 1, no. 1 (2021): 1–14. http://dx.doi.org/10.3390/biophysica1010001.

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Per-Arnt-Sim (PAS) domains are evolutionarily-conserved regions found in proteins in all living systems, involved in transcriptional regulation and the response to hypoxic and xenobiotic stress. Despite having low primary sequence similarity, they show an impressively high structural conservation. Nonetheless, understanding the underlying mechanisms that drive the biological function of the PAS domains remains elusive. In this work, we used molecular dynamics simulations and bioinformatics tools in order the investigate the molecular characteristics that govern the intrinsic dynamics of five P

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14

Xu, Xingjian, Igor Dikiy, Matthew R. Evans, Leandro P. Marcelino, and Kevin H. Gardner. "Fragile protein folds: sequence and environmental factors affecting the equilibrium of two interconverting, stably folded protein conformations." Magnetic Resonance 2, no. 1 (2021): 63–76. http://dx.doi.org/10.5194/mr-2-63-2021.

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Abstract. Recent research on fold-switching metamorphic proteins has revealed some notable exceptions to Anfinsen's hypothesis of protein folding. We have previously described how a single point mutation can enable a well-folded protein domain, one of the two PAS (Per-ARNT-Sim) domains of the human ARNT (aryl hydrocarbon receptor nuclear translocator) protein, to interconvert between two conformers related by a slip of an internal β strand. Using this protein as a test case, we advance the concept of a “fragile fold”, a protein fold that can reversibly rearrange into another fold that differs

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15

Gradin, K., J. McGuire, R. H. Wenger, et al. "Functional interference between hypoxia and dioxin signal transduction pathways: competition for recruitment of the Arnt transcription factor." Molecular and Cellular Biology 16, no. 10 (1996): 5221–31. http://dx.doi.org/10.1128/mcb.16.10.5221.

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Hypoxia-inducible factor 1 alpha (HIF-1 alpha) and the intracellular dioxin receptor mediate hypoxia and dioxin signalling, respectively. Both proteins are conditionally regulated basic helix-loop-helix (bHLH) transcription factors that, in addition to the bHLH motif, share a Per-Arnt-Sim (PAS) region of homology and form heterodimeric complexes with the common bHLH/PAS partner factor Arnt. Here we demonstrate that HIF-1 alpha required Arnt for DNA binding in vitro and functional activity in vivo. Both the bHLH and PAS motifs of Arnt were critical for dimerization with HIF-1 alpha. Strikingly,

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16

Aitola, Marjo, Christine M. Sadek, Jan-Åke Gustafsson, and Markku Pelto-Huikko. "Aint/Tacc3 Is Highly Expressed in Proliferating Mouse Tissues During Development, Spermatogenesis, and Oogenesis." Journal of Histochemistry & Cytochemistry 51, no. 4 (2003): 455–69. http://dx.doi.org/10.1177/002215540305100407.

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Aint was originally identified on the basis of its interaction in vitro with the aryl hydrocarbon nuclear receptor translocator (Arnt). Arnt is a common heterodimerization partner in the basic helix-loop–helix (bHLH)-PER-ARNT-SIM (PAS) protein family and is involved in diverse biological functions. These include xenobiotic metabolism, hypoxic response, and circadian rhythm. In addition, Arnt has a crucial role during development. Aint is a member of a growing family of transforming acidic coiled-coil (TACC) proteins and is the murine homologue of human TACC3. Here we report the spatiotemporal

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17

Seok, Seung-Hyeon, Woojong Lee, Li Jiang, et al. "Structural hierarchy controlling dimerization and target DNA recognition in the AHR transcriptional complex." Proceedings of the National Academy of Sciences 114, no. 21 (2017): 5431–36. http://dx.doi.org/10.1073/pnas.1617035114.

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The aryl hydrocarbon receptor (AHR) belongs to the PAS (PER-ARNT-SIM) family transcription factors and mediates broad responses to numerous environmental pollutants and cellular metabolites, modulating diverse biological processes from adaptive metabolism, acute toxicity, to normal physiology of vascular and immune systems. The AHR forms a transcriptionally active heterodimer with ARNT (AHR nuclear translocator), which recognizes the dioxin response element (DRE) in the promoter of downstream genes. We determined the crystal structure of the mammalian AHR–ARNT heterodimer in complex with the D

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18

Antonsson, C., M. L. Whitelaw, J. McGuire, J. A. Gustafsson, and L. Poellinger. "Distinct roles of the molecular chaperone hsp90 in modulating dioxin receptor function via the basic helix-loop-helix and PAS domains." Molecular and Cellular Biology 15, no. 2 (1995): 756–65. http://dx.doi.org/10.1128/mcb.15.2.756.

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The intracellular dioxin receptor mediates signal transduction by dioxin and functions as a ligand-activated transcription factor. It contains a basic helix-loop-helix (bHLH) motif contiguous with a Per-Arnt-Sim (PAS) homology region. In extracts from nonstimulated cells the receptor is recovered in an inducible cytoplasmic form associated with the 90-kDa heat shock protein (hsp90), a molecular chaperone. We have reconstituted ligand-dependent activation of the receptor to a DNA-binding form by using the dioxin receptor and its bHLH-PAS partner factor Arnt expressed by in vitro translation in

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19

Semplici, Francesca, Martine Vaxillaire, Sarah Fogarty, et al. "Human Mutation within Per-Arnt-Sim (PAS) Domain-containing Protein Kinase (PASK) Causes Basal Insulin Hypersecretion." Journal of Biological Chemistry 286, no. 51 (2011): 44005–14. http://dx.doi.org/10.1074/jbc.m111.254995.

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20

Dardente, Hugues, Erin E. Fortier, Vincent Martineau, and Nicolas Cermakian. "Cryptochromes impair phosphorylation of transcriptional activators in the clock: a general mechanism for circadian repression." Biochemical Journal 402, no. 3 (2007): 525–36. http://dx.doi.org/10.1042/bj20060827.

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CLOCK and BMAL1 [brain and muscle ARNT (arylhydrocarbon receptor nuclear translocator)-like protein 1] are central components of the molecular clock in mammals and belong to the bHLH (basic helix–loop–helix)/PAS [PER (Period)/ARNT/SIM (single-minded)] family. Features of their dimerization have never been investigated. Here, we demonstrate that PAS domain function requires regions extending over the short PAS core repeats. Strikingly, while deleting PAS core repeats does not overtly affect dimerization, it abolishes the transcriptional activity of the heterodimer. Interestingly, these deletion

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21

Brody, Stuart. "A Comparison of the Neurospora and Drosophila Clocks." Journal of Biological Rhythms 35, no. 2 (2019): 119–33. http://dx.doi.org/10.1177/0748730419892434.

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In Neurospora and other fungi, the protein frequency (FRQ) is an integral part and a negative element in the fungal circadian oscillator. In Drosophila and many other higher organisms, the protein period (PER) is an integral part and a negative element of their circadian oscillator. Employing bioinformatic techniques, such as BLAST, CLUSTAL, and MEME (Multiple Em for Motif Elicitation), 11 regions (sequences) of potential similarity were found between the fungal FRQ and the Drosophila PER. Many of these FRQ regions are conserved in many fungal FRQ(s). Many of these PER regions are conserved in

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22

Chapman-Smith, Anne, Jodi K. Lutwyche, and Murray L. Whitelaw. "Contribution of the Per/Arnt/Sim (PAS) Domains to DNA Binding by the Basic Helix-Loop-Helix PAS Transcriptional Regulators." Journal of Biological Chemistry 279, no. 7 (2003): 5353–62. http://dx.doi.org/10.1074/jbc.m310041200.

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23

Bersten, David C., John B. Bruning, Daniel J. Peet, and Murray L. Whitelaw. "Human Variants in the Neuronal Basic Helix-Loop-Helix/Per-Arnt-Sim (bHLH/PAS) Transcription Factor Complex NPAS4/ARNT2 Disrupt Function." PLoS ONE 9, no. 1 (2014): e85768. http://dx.doi.org/10.1371/journal.pone.0085768.

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24

Gozu, Yoko, Junichi Hosoi, Hiroaki Nagatomo, Kayako Ishimaru, and Atsuhito Nakao. "The PAS-B Domain of BMAL1 Controls Proliferation, Cellular Energetics, and Inflammatory Response in Human Monocytic Cell Line THP-1." International Journal of Molecular Sciences 26, no. 14 (2025): 6737. https://doi.org/10.3390/ijms26146737.

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Brain muscle ARNT-like1 (Bmal1) is a transcriptional factor, consisting of basic helix–loop–helix (bHLH) and PER-ARNT-SIM (PAS) domains, that plays a central role in circadian clock activity. However, the precise roles of the BMAL1-PAS domain, a circadian rhythm-regulating structure, remain unexplored in monocytes. Here, we highlight the BMAL1-PAS domain as a key structure in monocyte pleiotropic functions by using human monocytic cell line THP-1. THP-1 cells lacking the BMAL1-PAS-B domain (THP-1#207) abrogated the circadian expression of core clock genes. THP-1#207 cells exhibited less prolif

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25

Coban, Mathew A., Patrick R. Blackburn, Murray L. Whitelaw, Mieke M. van Haelst, Paldeep S. Atwal, and Thomas R. Caulfield. "Structural Models for the Dynamic Effects of Loss-of-Function Variants in the Human SIM1 Protein Transcriptional Activation Domain." Biomolecules 10, no. 9 (2020): 1314. http://dx.doi.org/10.3390/biom10091314.

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Single-minded homologue 1 (SIM1) is a transcription factor with numerous different physiological and developmental functions. SIM1 is a member of the class I basic helix-loop-helix-PER-ARNT-SIM (bHLH–PAS) transcription factor family, that includes several other conserved proteins, including the hypoxia-inducible factors, aryl hydrocarbon receptor, neuronal PAS proteins, and the CLOCK circadian regulator. Recent studies of HIF-a-ARNT and CLOCK-BMAL1 protein complexes have revealed the organization of their bHLH, PASA, and PASB domains and provided insight into how these heterodimeric protein co

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26

Beischlag, Timothy V., Song Wang, David W. Rose, et al. "Recruitment of the NCoA/SRC-1/p160 Family of Transcriptional Coactivators by the Aryl Hydrocarbon Receptor/Aryl Hydrocarbon Receptor Nuclear Translocator Complex." Molecular and Cellular Biology 22, no. 12 (2002): 4319–33. http://dx.doi.org/10.1128/mcb.22.12.4319-4333.2002.

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ABSTRACT The aryl hydrocarbon receptor complex heterodimeric transcription factor, comprising the basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain aryl hydrocarbon receptor (AHR) and aryl hydrocarbon receptor nuclear translocator (ARNT) proteins, mediates the toxic effects of TCDD (2,3,7,8 tetrachlorodibenzo-p-dioxin). The molecular events underlying TCDD-inducible gene activation, beyond the activation of the AHRC, are poorly understood. The SRC-1/NCoA-1, NCoA-2/GRIP-1/TIF-2, and p/CIP/AIB/ACTR proteins have been shown to act as mediators of transcriptional activation. In this report, we

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Yamashita, Toshiharu, Osamu Ohneda, Masumi Nagano, et al. "Abnormal Heart Development and Lung Remodeling in Mice Lacking the Hypoxia-Inducible Factor-Related Basic Helix-Loop-Helix PAS Protein NEPAS." Molecular and Cellular Biology 28, no. 4 (2007): 1285–97. http://dx.doi.org/10.1128/mcb.01332-07.

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ABSTRACT Hypoxia-inducible factors (HIFs) are crucial for oxygen homeostasis during both embryonic development and postnatal life. Here we show that a novel HIF family basic helix-loop-helix (bHLH) PAS (Per-Arnt-Sim) protein, which is expressed predominantly during embryonic and neonatal stages and thereby designated NEPAS (neonatal and embryonic PAS), acts as a negative regulator of HIF-mediated gene expression. NEPAS mRNA is derived from the HIF-3α gene by alternative splicing, replacing the first exon of HIF-3α with that of inhibitory PAS. NEPAS can dimerize with Arnt and exhibits only low

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28

Giordano, Deborah, Angelo Facchiano, Stefania Moccia, Anna Maria Iole Meola, Gian Luigi Russo, and Carmela Spagnuolo. "Molecular Docking of Natural Compounds for Potential Inhibition of AhR." Foods 12, no. 10 (2023): 1953. http://dx.doi.org/10.3390/foods12101953.

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The aryl hydrocarbon receptor (AhR) is a highly conserved environmental sensor, historically known for mediating the toxicity of xenobiotics. It is involved in numerous cellular processes such as differentiation, proliferation, immunity, inflammation, homeostasis, and metabolism. It exerts a central role in several conditions such as cancer, inflammation, and aging, acting as a transcription factor belonging to the basic helix–loop–helix/Per-ARNT-Sim (bHLH-PAS) protein family. A key step in the canonical AhR activation is AhR-ARNT heterodimerization followed by the binding to the xenobiotic-re

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Yun, Jaesuk, Taku Nagai, Yoko Furukawa-Hibi, et al. "Neuronal Per Arnt Sim (PAS) Domain Protein 4 (NPAS4) Regulates Neurite Outgrowth and Phosphorylation of Synapsin I." Journal of Biological Chemistry 288, no. 4 (2012): 2655–64. http://dx.doi.org/10.1074/jbc.m112.413310.

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Liu, Yu C., Mayra A. Machuca, Simone A. Beckham, Menachem J. Gunzburg, and Anna Roujeinikova. "Structural basis for amino-acid recognition and transmembrane signalling by tandem Per–Arnt–Sim (tandem PAS) chemoreceptor sensory domains." Acta Crystallographica Section D Biological Crystallography 71, no. 10 (2015): 2127–36. http://dx.doi.org/10.1107/s139900471501384x.

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Chemotaxis, mediated by methyl-accepting chemotaxis protein (MCP) receptors, plays an important role in the ecology of bacterial populations. This paper presents the first crystallographic analysis of the structure and ligand-induced conformational changes of the periplasmic tandem Per-Arnt-Sim (PAS) sensing domain (PTPSD) of a characterized MCP chemoreceptor. Analysis of the complex of theCampylobacter jejuniTlp3 PTPSD with isoleucine (a chemoattractant) revealed that the PTPSD is a dimer in the crystal. The two ligand-binding sites are located in the membrane-distal PAS domains on the faces

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Tang, Xue, Juan Shao, and Xiaohong Qin. "Crystal structure of the PAS domain of the hEAG potassium channel." Acta Crystallographica Section F Structural Biology Communications 72, no. 8 (2016): 578–85. http://dx.doi.org/10.1107/s2053230x16009419.

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KCNH voltage-gated potassium channels play critical roles in regulating cellular functions. The channel is composed of four subunits, each of which contains six transmembrane helices forming the central pore. The cytoplasmic parts of the subunits present a Per–Arnt–Sim (PAS) domain at the N-terminus and a cyclic nucleotide-binding homology domain at the C-terminus. PAS domains are conserved from prokaryotes to eukaryotes and are involved in sensing signals and cellular responses. To better understand the functional roles of PAS domains in KCNH channels, the structure of this domain from the hu

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Gilles-Gonzalez, Marie-Alda, and Gonzalo Gonzalez. "Signal transduction by heme-containing PAS-domain proteins." Journal of Applied Physiology 96, no. 2 (2004): 774–83. http://dx.doi.org/10.1152/japplphysiol.00941.2003.

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The most common physiological strategy for detecting the gases oxygen, carbon monoxide, and nitric oxide is signal transduction by heme-based sensors, a broad class of modular proteins in which a heme-binding domain governs the activity of a neighboring transmitter domain. Different structures are possible for the heme-binding domains in these sensors, but, so far, the Per-ARNT-Sim motif, or PAS domain, is the one most commonly encountered. Heme-binding PAS (heme-PAS) domains can accomplish ligand-dependent switching of a variety of partner domains, including histidine kinase, phosphodiesteras

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An, R., G. da Silva Xavier, H. X. Hao, F. Semplici, J. Rutter та G. A. Rutter. "Regulation by Per-Arnt-Sim (PAS) kinase of pancreatic duodenal homeobox-1 nuclear import in pancreatic β-cells". Biochemical Society Transactions 34, № 5 (2006): 791–93. http://dx.doi.org/10.1042/bst0340791.

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The transcription factor PDX-1 (pancreatic duodenal homeobox-1) is required for normal pancreatic development and for the function of insulin-producing islet β-cells in mammals. We have shown previously that glucose regulates insulin gene expression in part through the activation and translocation of PDX-1 from the nuclear periphery to the nucleoplasm. We have also found that PASK [PAS (Per-Arnt-Sim) kinase], a member of the nutrient-regulated family of protein kinases, is activated in response to glucose challenge in β-cells and is involved in the regulation of expression of PDX-1. Purified P

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Militi, Stefania, Elizabeth S. Maywood, Colby R. Sandate, et al. "Early doors (Edo) mutant mouse reveals the importance of period 2 (PER2) PAS domain structure for circadian pacemaking." Proceedings of the National Academy of Sciences 113, no. 10 (2016): 2756–61. http://dx.doi.org/10.1073/pnas.1517549113.

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The suprachiasmatic nucleus (SCN) defines 24 h of time via a transcriptional/posttranslational feedback loop in which transactivation of Per (period) and Cry (cryptochrome) genes by BMAL1–CLOCK complexes is suppressed by PER–CRY complexes. The molecular/structural basis of how circadian protein complexes function is poorly understood. We describe a novel N-ethyl-N-nitrosourea (ENU)-induced mutation, early doors (Edo), in the PER-ARNT-SIM (PAS) domain dimerization region of period 2 (PER2) (I324N) that accelerates the circadian clock of Per2Edo/Edo mice by 1.5 h. Structural and biophysical anal

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Kolonko, Marta, and Beata Greb-Markiewicz. "bHLH–PAS Proteins: Their Structure and Intrinsic Disorder." International Journal of Molecular Sciences 20, no. 15 (2019): 3653. http://dx.doi.org/10.3390/ijms20153653.

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The basic helix–loop–helix/Per-ARNT-SIM (bHLH–PAS) proteins are a class of transcriptional regulators, commonly occurring in living organisms and highly conserved among vertebrates and invertebrates. These proteins exhibit a relatively well-conserved domain structure: the bHLH domain located at the N-terminus, followed by PAS-A and PAS-B domains. In contrast, their C-terminal fragments present significant variability in their primary structure and are unique for individual proteins. C-termini were shown to be responsible for the specific modulation of protein action. In this review, we present

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DeMille, Desiree, Benjamin T. Bikman, Andrew D. Mathis, et al. "A comprehensive protein–protein interactome for yeast PAS kinase 1 reveals direct inhibition of respiration through the phosphorylation of Cbf1." Molecular Biology of the Cell 25, no. 14 (2014): 2199–215. http://dx.doi.org/10.1091/mbc.e13-10-0631.

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Per-Arnt-Sim (PAS) kinase is a sensory protein kinase required for glucose homeostasis in yeast, mice, and humans, yet little is known about the molecular mechanisms of its function. Using both yeast two-hybrid and copurification approaches, we identified the protein–protein interactome for yeast PAS kinase 1 (Psk1), revealing 93 novel putative protein binding partners. Several of the Psk1 binding partners expand the role of PAS kinase in glucose homeostasis, including new pathways involved in mitochondrial metabolism. In addition, the interactome suggests novel roles for PAS kinase in cell gr

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Ke, Ying, Chai Ann Ng, Mark J. Hunter, et al. "Trafficking defects in PAS domain mutant Kv11.1 channels: roles of reduced domain stability and altered domain–domain interactions." Biochemical Journal 454, no. 1 (2013): 69–77. http://dx.doi.org/10.1042/bj20130328.

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Loss of Kv11.1 potassium channel function is the underlying cause of pathology in long-QT syndrome type 2, one of the commonest causes of sudden cardiac death in the young. Previous studies have identified the cytosolic PAS (Per/Arnt/Sim) domain as a hotspot for mutations that cause Kv11.1 trafficking defects. To investigate the underlying basis of this observation, we have quantified the effect of mutants on domain folding as well as interactions between the PAS domain and the remainder of the channel. Apart from R56Q, all mutants impaired the thermostability of the isolated PAS domain. Six m

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Chen, Jun, Anrou Zou, Igor Splawski, Mark T. Keating, and Michael C. Sanguinetti. "Long QT Syndrome-associated Mutations in the Per-Arnt-Sim (PAS) Domain of HERG Potassium Channels Accelerate Channel Deactivation." Journal of Biological Chemistry 274, no. 15 (1999): 10113–18. http://dx.doi.org/10.1074/jbc.274.15.10113.

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Harley, Carol A., Greg Starek, David K. Jones, Andreia S. Fernandes, Gail A. Robertson, and João H. Morais-Cabral. "Enhancement of hERG channel activity by scFv antibody fragments targeted to the PAS domain." Proceedings of the National Academy of Sciences 113, no. 35 (2016): 9916–21. http://dx.doi.org/10.1073/pnas.1601116113.

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The human human ether-à-go-go–related gene (hERG) potassium channel plays a critical role in the repolarization of the cardiac action potential. Changes in hERG channel function underlie long QT syndrome (LQTS) and are associated with cardiac arrhythmias and sudden death. A striking feature of this channel and KCNH channels in general is the presence of an N-terminal Per-Arnt-Sim (PAS) domain. In other proteins, PAS domains bind ligands and modulate effector domains. However, the PAS domains of KCNH channels are orphan receptors. We have uncovered a family of positive modulators of hERG that s

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Pape, Jenny, Colleen Newey, Haley Burrell, et al. "Per-Arnt-Sim Kinase (PASK) Deficiency Increases Cellular Respiration on a Standard Diet and Decreases Liver Triglyceride Accumulation on a Western High-Fat High-Sugar Diet." Nutrients 10, no. 12 (2018): 1990. http://dx.doi.org/10.3390/nu10121990.

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Diabetes and the related disease metabolic syndrome are epidemic in the United States, in part due to a shift in diet and decrease in physical exercise. PAS kinase is a sensory protein kinase associated with many of the phenotypes of these diseases, including hepatic triglyceride accumulation and metabolic dysregulation in male mice placed on a high-fat diet. Herein we provide the first characterization of the effects of western diet (high-fat high-sugar, HFHS) on Per-Arnt-Sim kinase mice (PASK−/−) and the first characterization of both male and female PASK−/− mice. Soleus muscle from the PASK

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Soshilov, Anatoly A., Stefano Motta, Laura Bonati, and Michael S. Denison. "Transitional States in Ligand-Dependent Transformation of the Aryl Hydrocarbon Receptor into Its DNA-Binding Form." International Journal of Molecular Sciences 21, no. 7 (2020): 2474. http://dx.doi.org/10.3390/ijms21072474.

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The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that mediates the biological and toxicological effects of an AhR lacking the entire PASB structurally diverse chemicals, including halogenated aromatic hydrocarbons. Ligand-dependent transformation of the AhR into its DNA binding form involves a ligand-dependent conformational change, heat shock protein 90 (hsp90), dissociation from the AhR complex and AhR dimerization with the AhR nuclear translocator (ARNT) protein. The mechanism of AhR transformation was examined using mutational approaches and stabilization of t

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Kolonko-Adamska, Marta, Vladimir N. Uversky, and Beata Greb-Markiewicz. "The Participation of the Intrinsically Disordered Regions of the bHLH-PAS Transcription Factors in Disease Development." International Journal of Molecular Sciences 22, no. 6 (2021): 2868. http://dx.doi.org/10.3390/ijms22062868.

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The basic helix–loop–helix/Per-ARNT-SIM (bHLH-PAS) proteins are a family of transcription factors regulating expression of a wide range of genes involved in different functions, ranging from differentiation and development control by oxygen and toxins sensing to circadian clock setting. In addition to the well-preserved DNA-binding bHLH and PAS domains, bHLH-PAS proteins contain long intrinsically disordered C-terminal regions, responsible for regulation of their activity. Our aim was to analyze the potential connection between disordered regions of the bHLH-PAS transcription factors, post-tra

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Burton, Mark J., Joel Cresser-Brown, Morgan Thomas, et al. "Discovery of a heme-binding domain in a neuronal voltage-gated potassium channel." Journal of Biological Chemistry 295, no. 38 (2020): 13277–86. http://dx.doi.org/10.1074/jbc.ra120.014150.

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The EAG (ether-à-go-go) family of voltage-gated K+ channels are important regulators of neuronal and cardiac action potential firing (excitability) and have major roles in human diseases such as epilepsy, schizophrenia, cancer, and sudden cardiac death. A defining feature of EAG (Kv10–12) channels is a highly conserved domain on the N terminus, known as the eag domain, consisting of a Per–ARNT–Sim (PAS) domain capped by a short sequence containing an amphipathic helix (Cap domain). The PAS and Cap domains are both vital for the normal function of EAG channels. Using heme-affinity pulldown assa

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Ke, Ying, Mark J. Hunter, Chai Ann Ng, Matthew D. Perry, and Jamie I. Vandenberg. "Role of the Cytoplasmic N-terminal Cap and Per-Arnt-Sim (PAS) Domain in Trafficking and Stabilization of Kv11.1 Channels." Journal of Biological Chemistry 289, no. 20 (2014): 13782–91. http://dx.doi.org/10.1074/jbc.m113.531277.

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Wang, Ze-Jun, Stephanie M. Soohoo, Purushottam B. Tiwari, Grzegorz Piszczek, and Tinatin I. Brelidze. "Chlorpromazine binding to the PAS domains uncovers the effect of ligand modulation on EAG channel activity." Journal of Biological Chemistry 295, no. 13 (2020): 4114–23. http://dx.doi.org/10.1074/jbc.ra119.012377.

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Ether-a-go-go (EAG) potassium selective channels are major regulators of neuronal excitability and cancer progression. EAG channels contain a Per–Arnt–Sim (PAS) domain in their intracellular N-terminal region. The PAS domain is structurally similar to the PAS domains in non-ion channel proteins, where these domains frequently function as ligand-binding domains. Despite the structural similarity, it is not known whether the PAS domain can regulate EAG channel function via ligand binding. Here, using surface plasmon resonance, tryptophan fluorescence, and analysis of EAG currents recorded in Xen

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Kikani, Chintan K. "Metabolic “Sense Relay” in Stem Cells: A Short But Impactful Life of PAS Kinase Balancing Stem Cell Fates." Cells 12, no. 13 (2023): 1751. http://dx.doi.org/10.3390/cells12131751.

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Tissue regeneration is a complex molecular and biochemical symphony. Signaling pathways establish the rhythmic proliferation and differentiation cadence of participating cells to repair the damaged tissues and repopulate the tissue-resident stem cells. Sensory proteins form a critical bridge between the environment and cellular response machinery, enabling precise spatiotemporal control of stem cell fate. Of many sensory modules found in proteins from prokaryotes to mammals, Per-Arnt-Sim (PAS) domains are one of the most ancient and found in the most diverse physiological context. In metazoa,

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Heintz, Udo, Anton Meinhart, and Andreas Winkler. "Multi-PAS domain-mediated protein oligomerization of PpsR fromRhodobacter sphaeroides." Acta Crystallographica Section D Biological Crystallography 70, no. 3 (2014): 863–76. http://dx.doi.org/10.1107/s1399004713033634.

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Per–ARNT–Sim (PAS) domains are essential modules of many multi-domain signalling proteins that mediate protein interaction and/or sense environmental stimuli. Frequently, multiple PAS domains are present within single polypeptide chains, where their interplay is required for protein function. Although many isolated PAS domain structures have been reported over the last decades, only a few structures of multi-PAS proteins are known. Therefore, the molecular mechanism of multi-PAS domain-mediated protein oligomerization and function is poorly understood. The transcription factor PpsR fromRhodoba

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Torii, Satoru, Shuya Kasai, Tatsushi Yoshida, Ken-ichi Yasumoto, and Shigeomi Shimizu. "Mitochondrial E3 Ubiquitin Ligase Parkin: Relationships with Other Causal Proteins in Familial Parkinson’s Disease and Its Substrate-Involved Mouse Experimental Models." International Journal of Molecular Sciences 21, no. 4 (2020): 1202. http://dx.doi.org/10.3390/ijms21041202.

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Parkinson’s disease (PD) is a common neurodegenerative disorder. Recent identification of genes linked to familial forms of PD has revealed that post-translational modifications, such as phosphorylation and ubiquitination of proteins, are key factors in disease pathogenesis. In PD, E3 ubiquitin ligase Parkin and the serine/threonine-protein kinase PTEN-induced kinase 1 (PINK1) mediate the mitophagy pathway for mitochondrial quality control via phosphorylation and ubiquitination of their substrates. In this review, we first focus on well-characterized PINK1 phosphorylation motifs. Second, we de

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Karakkat, Jimsheena V., Suneesh Kaimala, Sreejisha P. Sreedharan, et al. "The metabolic sensor PASK is a histone 3 kinase that also regulates H3K4 methylation by associating with H3K4 MLL2 methyltransferase complex." Nucleic Acids Research 47, no. 19 (2019): 10086–103. http://dx.doi.org/10.1093/nar/gkz786.

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Abstract The metabolic sensor Per-Arnt-Sim (Pas) domain-containing serine/threonine kinase (PASK) is expressed predominantly in the cytoplasm of different cell types, although a small percentage is also expressed in the nucleus. Herein, we show that the nuclear PASK associates with the mammalian H3K4 MLL2 methyltransferase complex and enhances H3K4 di- and tri-methylation. We also show that PASK is a histone kinase that phosphorylates H3 at T3, T6, S10 and T11. Taken together, these results suggest that PASK regulates two different H3 tail modifications involving H3K4 methylation and H3 phosph

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da Silva Xavier, G., J. Rutter, and G. A. Rutter. "Involvement of Per-Arnt-Sim (PAS) kinase in the stimulation of preproinsulin and pancreatic duodenum homeobox 1 gene expression by glucose." Proceedings of the National Academy of Sciences 101, no. 22 (2004): 8319–24. http://dx.doi.org/10.1073/pnas.0307737101.

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