Human Sirt-1: Molecular Modeling and Structure-Function Relationships of an Unordered Protein

Autiero, Ida; Costantini, Susan; Colonna, Giovanni

doi:10.1371/journal.pone.0007350

Cited by 63 publications

(55 citation statements)

References 59 publications

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“…Since Sirtuin catalytic domains have been described as monomers [8,54], the Sirt1 termini might mediate oligomerization. Our experiments show, however, that Sirt1 is a monomer that migrates fast in SEC due to an extended conformation, apparently mainly due to a disordered N-terminus, consistent with bioinformatics analyses reported here and previously [55]. The C-terminus also appears to harbour disordered regions, but partially seems to adopt a defined conformation that interacts with the catalytic core [17].…”

Section: Discussionsupporting

confidence: 90%

Molecular architecture of the human protein deacetylase Sirt1 and its regulation by AROS and resveratrol

et al. 2013

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Sirtuins are NAD+-dependent protein deacetylases regulating metabolism, stress responses and ageing processes. Among the seven mammalian Sirtuins, Sirt1 is the physiologically best-studied isoform. It regulates nuclear functions such as chromatin remodelling and gene transcription, and it appears to mediate beneficial effects of a low calorie diet which can partly be mimicked by the Sirt1 activating polyphenol resveratrol. The molecular details of Sirt1 domain architecture and regulation, however, are little understood. It has a unique N-terminal domain and CTD (C-terminal domain) flanking a conserved Sirtuin catalytic core and these extensions are assumed to mediate Sirt1-specific features such as homo-oligomerization and activation by resveratrol. To analyse the architecture of human Sirt1 and functions of its N- and C-terminal extensions, we recombinantly produced Sirt1 and Sirt1 deletion constructs as well as the AROS (active regulator of Sirt1) protein. We then studied Sirt1 features such as molecular size, secondary structure and stimulation by small molecules and AROS. We find that Sirt1 is monomeric and has extended conformations in its flanking domains, likely disordered especially in the N-terminus, resulting in an increased hydrodynamic radius. Nevertheless, both termini increase Sirt1 deacetylase activity, indicating a regulatory function. We also find an unusual but defined conformation for AROS protein, which fails, however, to stimulate Sirt1. Resveratrol, in contrast, activates the Sirt1 catalytic core independent of the terminal domains, indicating a binding site within the catalytic core and suggesting that small molecule activators for other isoforms might also exist.

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Section: Discussionsupporting

confidence: 90%

Molecular architecture of the human protein deacetylase Sirt1 and its regulation by AROS and resveratrol

et al. 2013

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“…The structure of the catalytic domain of model sirtuins has been solved, 101 but computational methods applied to the full-length SIRT1 sequence indicate that the N-and C-terminal portions of the protein are largely unstructured, 102 which is an observation consistent with the idea that SIRT1 can interact with a vast array of different proteins by "coupled binding and folding. " Bioinformatic analysis of proteins found to contain large unstructured regions (designated intrinsically disordered proteins, or IDPs) has revealed that they are highly enriched in proteins that are network hubs.…”

Section: Sirt1 Is a Protein Network Hubmentioning

confidence: 84%

SIRT1 is a Highly Networked Protein That Mediates the Adaptation to Chronic Physiological Stress

et al. 2013

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SIRT1 is a NAD + -dependent protein deacetylase that has a very large number of established protein substrates and an equally impressive list of biological functions thought to be regulated by its activity. Perhaps as notable is the remarkable number of points of conflict concerning the role of SIRT1 in biological processes. For example, evidence exists suggesting that SIRT1 is a tumor suppressor, is an oncogene, or has no effect on oncogenesis. Similarly, SIRT1 is variably reported to induce, inhibit, or have no effect on autophagy. We believe that the resolution of many conflicting results is possible by considering recent reports indicating that SIRT1 is an important hub interacting with a complex network of proteins that collectively regulate a wide variety of biological processes including cancer and autophagy. A number of the interacting proteins are themselves hubs that, like SIRT1, utilize intrinsically disordered regions for their promiscuous interactions. Many studies investigating SIRT1 function have been carried out on cell lines carrying undetermined numbers of alterations to the proteins comprising the SIRT1 network or on inbred mouse strains carrying fixed mutations affecting some of these proteins. Thus, the effects of modulating SIRT1 amount and/or activity are importantly determined by the genetic background of the cell (or the inbred strain of mice), and the effects attributed to SIRT1 are synthetic with the background of mutations and epigenetic differences between cells and organisms. Work on mice carrying alterations to the Sirt1 gene suggests that the network in which SIRT1 functions plays an important role in mediating physiological adaptation to various sources of chronic stress such as calorie restriction and calorie overload. Whether the catalytic activity of SIRT1 and the nuclear concentration of the co-factor, NAD + , are responsible for modulating this activity remains to be determined. However, the effect of modulating SIRT1 activity must be interpreted in the context of the cell or tissue under investigation. Indeed, for SIRT1, we argue that context is everything.

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“…Human SirT1 consists of 747 amino acids, divided into four major regions: N-terminal domain (residues 1–182), allosteric site (residues 183–243), catalytic core (residues 244–498) and C-terminal domain (residues 499–747) (25). SirT1 catalyzes the protein deacetylation reaction in its catalytic core, which consists of two subdomains for NAD + and substrate binding (26).…”

Section: Discussionmentioning

confidence: 99%

SirT1 activator represses the transcription of TNF-α in THP-1 cells of a sepsis model via deacetylation of H4K16

Chen

2016

Molecular Medicine Reports

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Sepsis is a systemic inflammatory response resulting from the excessive production of pro-inflammatory cytokines, including tumor necrosis factor (TNF)-α. Sirtuin 1 (SirT1) actively deacetylates histone proteins, and facilitates chromatin compaction and gene silencing. In the present study, a cell model of sepsis, comprising lipopolysaccharide (LPS)-tolerant THP-1 cells, was used to investigate whether the SirT1 activator, resveratrol, repressed the transcription of TNF-α. Chromatin immunoprecipitation and real-time PCR were used to determine the transcription of the TNF-α promoter. The result revealed that the binding of SirT1 to the TNF-α promoter was decreased by LPS stimulation in normal cells. However, in LPS-tolerant cells, nuclear protein levels of SirT1 remained elevated, and LPS stimulation had no significant effect on the binding of SirT1 to the TNF-α promoter. However, the activity of SirT1 was increased and binding of ace-H4K16 to the TNF-α promoter was decreased with resveratrol treatment in the tolerant cells. It was concluded that resveratrol stimulated sirtuin activity in LPS-tolerant THP-1 cells, and repressed TNF-α transcription through the deacetylation of H4K16, without affecting the methylation of H3K9. Resveratrol offers potential as an infective candidate to alleviate inflammation in patients with sepsis.

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Human Sirt-1: Molecular Modeling and Structure-Function Relationships of an Unordered Protein

Cited by 63 publications

References 59 publications

Molecular architecture of the human protein deacetylase Sirt1 and its regulation by AROS and resveratrol

Molecular architecture of the human protein deacetylase Sirt1 and its regulation by AROS and resveratrol

SIRT1 is a Highly Networked Protein That Mediates the Adaptation to Chronic Physiological Stress

SirT1 activator represses the transcription of TNF-α in THP-1 cells of a sepsis model via deacetylation of H4K16

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