Regulation of apoptosis by an intrinsically disordered region of Bcl-xL.

Abstract:

:Intrinsically disordered regions (IDRs) of proteins often regulate function upon post-translational modification (PTM) through interactions with folded domains. An IDR linking two α-helices (α1-α2) of the antiapoptotic protein Bcl-xL experiences several PTMs that reduce antiapoptotic activity. Here, we report that PTMs within the α1-α2 IDR promote its interaction with the folded core of Bcl-xL that inhibits the proapoptotic activity of two types of regulatory targets, BH3-only proteins and p53. This autoregulation utilizes an allosteric pathway whereby, in one direction, the IDR induces a direct displacement of p53 from Bcl-xL coupled to allosteric displacement of simultaneously bound BH3-only partners. This pathway operates in the opposite direction when the BH3-only protein PUMA binds to the BH3 binding groove of Bcl-xL, directly displacing other bound BH3-only proteins, and allosterically remodels the distal site, displacing p53. Our findings show how an IDR enhances functional versatility through PTM-dependent allosteric regulation of a folded protein domain.

journal_name

Nat Chem Biol

journal_title

Nature chemical biology

authors

Follis AV,Llambi F,Kalkavan H,Yao Y,Phillips AH,Park CG,Marassi FM,Green DR,Kriwacki RW

doi

10.1038/s41589-018-0011-x

subject

Has Abstract

pub_date

2018-05-01 00:00:00

pages

458-465

issue

5

eissn

1552-4450

issn

1552-4469

pii

10.1038/s41589-018-0011-x

journal_volume

14

pub_type

杂志文章
  • Small molecule-triggered Cas9 protein with improved genome-editing specificity.

    abstract::Directly modulating the activity of genome-editing proteins has the potential to increase their specificity by reducing activity following target locus modification. We developed Cas9 nucleases that are activated by the presence of a cell-permeable small molecule by inserting an evolved 4-hydroxytamoxifen-responsive i...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1793

    authors: Davis KM,Pattanayak V,Thompson DB,Zuris JA,Liu DR

    更新日期:2015-05-01 00:00:00

  • Cleavage of a carbon-fluorine bond by an engineered cysteine dioxygenase.

    abstract::Cysteine dioxygenase (CDO) plays an essential role in sulfur metabolism by regulating homeostatic levels of cysteine. Human CDO contains a post-translationally generated Cys93-Tyr157 cross-linked cofactor. Here, we investigated this Cys-Tyr cross-linking by incorporating unnatural tyrosines in place of Tyr157 via a ge...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/s41589-018-0085-5

    authors: Li J,Griffith WP,Davis I,Shin I,Wang J,Li F,Wang Y,Wherritt DJ,Liu A

    更新日期:2018-09-01 00:00:00

  • Structural basis for halogenation by iron- and 2-oxo-glutarate-dependent enzyme WelO5.

    abstract::A 2.4-Å-resolution X-ray crystal structure of the carrier-protein-independent halogenase WelO5 in complex with its welwitindolinone precursor substrate, 12-epi-fischerindole U, reveals that the C13 chlorination target is proximal to the anticipated site of the oxo group in a presumptive cis-halo-oxo-iron(IV) (haloferr...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2112

    authors: Mitchell AJ,Zhu Q,Maggiolo AO,Ananth NR,Hillwig ML,Liu X,Boal AK

    更新日期:2016-08-01 00:00:00

  • Suppressors of superoxide production from mitochondrial complex III.

    abstract::Mitochondrial electron transport drives ATP synthesis but also generates reactive oxygen species, which are both cellular signals and damaging oxidants. Superoxide production by respiratory complex III is implicated in diverse signaling events and pathologies, but its role remains controversial. Using high-throughput ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1910

    authors: Orr AL,Vargas L,Turk CN,Baaten JE,Matzen JT,Dardov VJ,Attle SJ,Li J,Quackenbush DC,Goncalves RL,Perevoshchikova IV,Petrassi HM,Meeusen SL,Ainscow EK,Brand MD

    更新日期:2015-11-01 00:00:00

  • Polypharmacology-based ceritinib repurposing using integrated functional proteomics.

    abstract::Targeted drugs are effective when they directly inhibit strong disease drivers, but only a small fraction of diseases feature defined actionable drivers. Alternatively, network-based approaches can uncover new therapeutic opportunities. Applying an integrated phenotypic screening, chemical and phosphoproteomics strate...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2489

    authors: Kuenzi BM,Remsing Rix LL,Stewart PA,Fang B,Kinose F,Bryant AT,Boyle TA,Koomen JM,Haura EB,Rix U

    更新日期:2017-12-01 00:00:00

  • Defining the geometry of the two-component proteasome degron.

    abstract::The eukaryotic 26S proteasome controls cellular processes by degrading specific regulatory proteins. Most proteins are targeted for degradation by a signal or degron that consists of two parts: a proteasome-binding tag, typically covalently attached polyubiquitin chains, and an unstructured region that serves as the i...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.521

    authors: Inobe T,Fishbain S,Prakash S,Matouschek A

    更新日期:2011-03-01 00:00:00

  • Autophagy induction enhances TDP43 turnover and survival in neuronal ALS models.

    abstract::Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) have distinct clinical features but a common pathology--cytoplasmic inclusions rich in transactive response element DNA-binding protein of 43 kDa (TDP43). Rare TDP43 mutations cause ALS or FTD, but abnormal TDP43 levels and localization may cause di...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1563

    authors: Barmada SJ,Serio A,Arjun A,Bilican B,Daub A,Ando DM,Tsvetkov A,Pleiss M,Li X,Peisach D,Shaw C,Chandran S,Finkbeiner S

    更新日期:2014-08-01 00:00:00

  • Optogenetic control of kinetochore function.

    abstract::Kinetochores act as hubs for multiple activities during cell division, including microtubule interactions and spindle checkpoint signaling. Each kinetochore can act autonomously, and activities change rapidly as proteins are recruited to, or removed from, kinetochores. Understanding this dynamic system requires tools ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2456

    authors: Zhang H,Aonbangkhen C,Tarasovetc EV,Ballister ER,Chenoweth DM,Lampson MA

    更新日期:2017-10-01 00:00:00

  • Confinement-induced quorum sensing of individual Staphylococcus aureus bacteria.

    abstract::It is postulated that in addition to cell density, other factors such as the dimensions and diffusional characteristics of the environment could influence quorum sensing (QS) and induction of genetic reprogramming. Modeling studies predict that QS may operate at the level of a single cell, but, owing to experimental c...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.264

    authors: Carnes EC,Lopez DM,Donegan NP,Cheung A,Gresham H,Timmins GS,Brinker CJ

    更新日期:2010-01-01 00:00:00

  • Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis.

    abstract::Biosynthesis enables renewable production of manifold compounds, yet often biosynthetic performance must be improved for it to be economically feasible. Nongenetic, cell-to-cell variations in protein and metabolite concentrations are naturally inherent, suggesting the existence of both high- and low-performance varian...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2046

    authors: Xiao Y,Bowen CH,Liu D,Zhang F

    更新日期:2016-05-01 00:00:00

  • A PCBP1-BolA2 chaperone complex delivers iron for cytosolic [2Fe-2S] cluster assembly.

    abstract::Hundreds of cellular proteins require iron cofactors for activity, and cells express systems for their assembly and distribution. Molecular details of the cytosolic iron pool used for iron cofactors are lacking, but iron chaperones of the poly(rC)-binding protein (PCBP) family play a key role in ferrous ion distributi...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/s41589-019-0330-6

    authors: Patel SJ,Frey AG,Palenchar DJ,Achar S,Bullough KZ,Vashisht A,Wohlschlegel JA,Philpott CC

    更新日期:2019-09-01 00:00:00

  • Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria.

    abstract::Phenylketonuria (PKU) is characterized by phenylalanine accumulation and progressive mental retardation caused by an unknown mechanism. We demonstrate that at pathological concentrations, phenylalanine self-assembles into fibrils with amyloid-like morphology and well-ordered electron diffraction. These assemblies are ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1002

    authors: Adler-Abramovich L,Vaks L,Carny O,Trudler D,Magno A,Caflisch A,Frenkel D,Gazit E

    更新日期:2012-08-01 00:00:00

  • Thiolutin is a zinc chelator that inhibits the Rpn11 and other JAMM metalloproteases.

    abstract::Thiolutin is a disulfide-containing antibiotic and anti-angiogenic compound produced by Streptomyces. Its biological targets are not known. We show that reduced thiolutin is a zinc chelator that inhibits the JAB1/MPN/Mov34 (JAMM) domain-containing metalloprotease Rpn11, a deubiquitinating enzyme of the 19S proteasome....

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2370

    authors: Lauinger L,Li J,Shostak A,Cemel IA,Ha N,Zhang Y,Merkl PE,Obermeyer S,Stankovic-Valentin N,Schafmeier T,Wever WJ,Bowers AA,Carter KP,Palmer AE,Tschochner H,Melchior F,Deshaies RJ,Brunner M,Diernfellner A

    更新日期:2017-07-01 00:00:00

  • DAGLβ inhibition perturbs a lipid network involved in macrophage inflammatory responses.

    abstract::The endocannabinoid 2-arachidonoylglycerol (2-AG) is biosynthesized by diacylglycerol lipases DAGLα and DAGLβ. Chemical probes to perturb DAGLs are needed to characterize endocannabinoid function in biological processes. Here we report a series of 1,2,3-triazole urea inhibitors, along with paired negative-control and ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1105

    authors: Hsu KL,Tsuboi K,Adibekian A,Pugh H,Masuda K,Cravatt BF

    更新日期:2012-12-01 00:00:00

  • A fluorescent probe for cysteine depalmitoylation reveals dynamic APT signaling.

    abstract::Hundreds of human proteins are modified by reversible palmitoylation of cysteine residues (S-palmitoylation), but the regulation of depalmitoylation is poorly understood. Here, we develop 'depalmitoylation probes' (DPPs), small-molecule fluorophores, to monitor the endogenous activity levels of 'erasers' of S-palmitoy...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2262

    authors: Kathayat RS,Elvira PD,Dickinson BC

    更新日期:2017-02-01 00:00:00

  • A new family of iron-dependent halogenases acts on freestanding substrates.

    abstract::Regio- and stereospecific incorporation of a halogen atom to an unactivated sp(3) carbon in a freestanding molecule is a challenging transformation that is currently missing in the inventory of enzyme-mediated reactions. Here we report what is to our knowledge the first example of a nonheme iron enzyme (WelO5) in the ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1625

    authors: Hillwig ML,Liu X

    更新日期:2014-11-01 00:00:00

  • Learning biological networks: from modules to dynamics.

    abstract::Learning regulatory networks from genomics data is an important problem with applications spanning all of biology and biomedicine. Functional genomics projects offer a cost-effective means of greatly expanding the completeness of our regulatory models, and for some prokaryotic organisms they offer a means of learning ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章,评审

    doi:10.1038/nchembio.122

    authors: Bonneau R

    更新日期:2008-11-01 00:00:00

  • Chemical hijacking of auxin signaling with an engineered auxin-TIR1 pair.

    abstract::The phytohormone auxin indole-3-acetic acid (IAA) regulates nearly all aspects of plant growth and development. Despite substantial progress in our understanding of auxin biology, delineating specific auxin response remains a major challenge. Auxin regulates transcriptional response via its receptors, TIR1 and AFB F-b...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2555

    authors: Uchida N,Takahashi K,Iwasaki R,Yamada R,Yoshimura M,Endo TA,Kimura S,Zhang H,Nomoto M,Tada Y,Kinoshita T,Itami K,Hagihara S,Torii KU

    更新日期:2018-03-01 00:00:00

  • Modulating the DNA polymerase β reaction equilibrium to dissect the reverse reaction.

    abstract::DNA polymerases catalyze efficient and high-fidelity DNA synthesis. While this reaction favors nucleotide incorporation, polymerases also catalyze a reverse reaction, pyrophosphorolysis, that removes the DNA primer terminus and generates deoxynucleoside triphosphates. Because pyrophosphorolysis can influence polymeras...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2450

    authors: Shock DD,Freudenthal BD,Beard WA,Wilson SH

    更新日期:2017-10-01 00:00:00

  • A broad HIV-1 inhibitor blocks envelope glycoprotein transitions critical for entry.

    abstract::Binding to the primary receptor, CD4, triggers conformational changes in the metastable HIV-1 envelope glycoprotein (Env) trimer ((gp120-gp41)3) that are important for virus entry into host cells. These changes include an 'opening' of the trimer, creation of a binding site for the CCR5 co-receptor and formation and/or...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1623

    authors: Herschhorn A,Gu C,Espy N,Richard J,Finzi A,Sodroski JG

    更新日期:2014-10-01 00:00:00

  • Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis.

    abstract::Hapalindole alkaloids are a structurally diverse class of cyanobacterial natural products defined by their varied polycyclic ring systems and diverse biological activities. These complex metabolites are generated from a common biosynthetic intermediate by the Stig cyclases in three mechanistic steps: a rare Cope rearr...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/s41589-018-0003-x

    authors: Newmister SA,Li S,Garcia-Borràs M,Sanders JN,Yang S,Lowell AN,Yu F,Smith JL,Williams RM,Houk KN,Sherman DH

    更新日期:2018-04-01 00:00:00

  • Grand challenge commentary: RNA epigenetics?

    abstract::Post-transcriptional RNA modifications can be dynamic and might have functions beyond fine-tuning the structure and function of RNA. Understanding these RNA modification pathways and their functions may allow researchers to identify new layers of gene regulation at the RNA level. ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.482

    authors: He C

    更新日期:2010-12-01 00:00:00

  • ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.

    abstract::The ykkC family of bacterial riboswitches combines several widespread classes that have similar secondary structures and consensus motifs but control different genes in response to different cellular metabolites. Here we report the crystal structures of two distinct ykkC riboswitches specifically bound to their cognat...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/s41589-018-0114-4

    authors: Peselis A,Serganov A

    更新日期:2018-09-01 00:00:00

  • Complete reconstitution of the diverse pathways of gentamicin B biosynthesis.

    abstract::Gentamicin B (GB), a valuable starting material for the preparation of the semisynthetic aminoglycoside antibiotic isepamicin, is produced in trace amounts by the wild-type Micromonospora echinospora. Though the biosynthetic pathway to GB has remained obscure for decades, we have now identified three hidden pathways t...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/s41589-018-0203-4

    authors: Ban YH,Song MC,Hwang JY,Shin HL,Kim HJ,Hong SK,Lee NJ,Park JW,Cha SS,Liu HW,Yoon YJ

    更新日期:2019-03-01 00:00:00

  • Targeted protein destabilization reveals an estrogen-mediated ER stress response.

    abstract::Accumulation of unfolded proteins within the endoplasmic reticulum (ER) of eukaryotic cells leads to an unfolded protein response (UPR) that either restores homeostasis or commits the cells to apoptosis. Tools traditionally used to study the UPR are proapoptotic and thus confound analysis of long-term cellular respons...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1638

    authors: Raina K,Noblin DJ,Serebrenik YV,Adams A,Zhao C,Crews CM

    更新日期:2014-11-01 00:00:00

  • Development of a covalent inhibitor of gut bacterial bile salt hydrolases.

    abstract::Bile salt hydrolase (BSH) enzymes are widely expressed by human gut bacteria and catalyze the gateway reaction leading to secondary bile acid formation. Bile acids regulate key metabolic and immune processes by binding to host receptors. There is an unmet need for a potent tool to inhibit BSHs across all gut bacteria ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/s41589-020-0467-3

    authors: Adhikari AA,Seegar TCM,Ficarro SB,McCurry MD,Ramachandran D,Yao L,Chaudhari SN,Ndousse-Fetter S,Banks AS,Marto JA,Blacklow SC,Devlin AS

    更新日期:2020-03-01 00:00:00

  • Diels-Alder reaction-triggered bioorthogonal protein decaging in living cells.

    abstract::Small molecules that specifically activate an intracellular protein of interest are highly desirable. A generally applicable strategy, however, remains elusive. Herein we describe a small molecule-triggered bioorthogonal protein decaging technique that relies on the inverse electron-demand Diels-Alder reaction for eli...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1656

    authors: Li J,Jia S,Chen PR

    更新日期:2014-12-01 00:00:00

  • Thioredoxin catalyzes the S-nitrosation of the caspase-3 active site cysteine.

    abstract::Nitric oxide (NO) signaling through the formation of cGMP is well established; however, there seems to be an increasing role for cGMP-independent NO signaling. Although key molecular details remain unanswered, S-nitrosation represents an example of cGMP-independent NO signaling. This modification has garnered recent a...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio720

    authors: Mitchell DA,Marletta MA

    更新日期:2005-08-01 00:00:00

  • Visualizing the secondary and tertiary architectural domains of lncRNA RepA.

    abstract::Long noncoding RNAs (lncRNAs) are important for gene expression, but little is known about their structures. RepA is a 1.6-kb mouse lncRNA comprising the same sequence as the 5' region of Xist, including A and F repeats. It has been proposed to facilitate the initiation and spread of X-chromosome inactivation, althoug...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2272

    authors: Liu F,Somarowthu S,Pyle AM

    更新日期:2017-03-01 00:00:00

  • Foldamers as versatile frameworks for the design and evolution of function.

    abstract::Foldamers are sequence-specific oligomers akin to peptides, proteins and oligonucleotides that fold into well-defined three-dimensional structures. They offer the chemical biologist a broad pallet of building blocks for the construction of molecules that test and extend our understanding of protein folding and functio...

    journal_title:Nature chemical biology

    pub_type: 杂志文章,评审

    doi:10.1038/nchembio876

    authors: Goodman CM,Choi S,Shandler S,DeGrado WF

    更新日期:2007-05-01 00:00:00