Signaling properties of a covalent modification cycle are altered by a downstream target.

Abstract:

:We used a model system of purified components to explore the effects of a downstream target on the signaling properties of a covalent modification cycle, an example of retroactivity. In the experimental system used, a bifunctional enzyme catalyzed the modification and demodification of its substrate protein, with both activities regulated by a small molecule stimulus. Here we examined how a downstream target for one or both forms of the substrate of the covalent modification cycle affected the steady-state output of the system, the sensitivity of the response to the stimulus, and the concentration of the stimulus required to provide the half-maximal response (S(50)). When both the modified and unmodified forms of the substrate protein were sequestered by the downstream target, the sensitivity of the response was dramatically decreased, but the S(50) was only modestly affected. Conversely, when the downstream target only sequestered the unmodified form of the substrate protein, significant effects were observed on both system sensitivity and S(50). Behaviors of the experimental systems were well approximated both by simple models allowing analytical solutions and by a detailed model based on the known interactions and enzymatic activities. Modeling and experimentation indicated that retroactivity may result in subsensitive responses, even if the covalent modification cycle displays significant ultrasensitivity in the absence of retroactivity. Thus, we provide examples of how a downstream target can alter the signaling properties of an upstream signal transduction covalent modification cycle.

authors

Ventura AC,Jiang P,Van Wassenhove L,Del Vecchio D,Merajver SD,Ninfa AJ

doi

10.1073/pnas.0913815107

subject

Has Abstract

pub_date

2010-06-01 00:00:00

pages

10032-7

issue

22

eissn

0027-8424

issn

1091-6490

pii

0913815107

journal_volume

107

pub_type

杂志文章
  • Genes encoding major light-harvesting polypeptides are clustered on the genome of the cyanobacterium Fremyella diplosiphon.

    abstract::The polypeptide composition of the phycobilisome, the major light-harvesting complex of prokaryotic cyanobacteria and certain eukaryotic algae, can be modulated by different light qualities in cyanobacteria exhibiting chromatic adaptation. We have identified genomic fragments encoding a cluster of phycobilisome polype...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.11.3924

    authors: Conley PB,Lemaux PG,Lomax TL,Grossman AR

    更新日期:1986-06-01 00:00:00

  • Calculations of the circular dichroism of adenosine derivatives constrained in the syn form.

    abstract::The rotational strengths of the four longer wavelength transitions, B(2u), B(1u), and the two E(1u), of adenosine derivatives constrained in the syn form have been investigated theoretically and experimentally. The theory combines a complete neglect of differential overlap version S (CNDO/S) description of the base wi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.6.3398

    authors: Miles DW,Farmer M,Eyring H

    更新日期:1980-06-01 00:00:00

  • The pre-S domain of the large viral envelope protein determines host range in avian hepatitis B viruses.

    abstract::In addition to their well-recognized hepatotropism, all hepatitis B viruses (HBVs) display marked species specificity, growing poorly or not at all in species other than those closely related to their natural hosts. We have examined the molecular basis for this narrow host range, using duck HBV (DHBV) and heron HBV (H...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.14.6259

    authors: Ishikawa T,Ganem D

    更新日期:1995-07-03 00:00:00

  • Bile acid metabolism in hereditary forms of hypertriglyceridemia: evidence for an increased synthesis rate in monogenic familial hypertriglyceridemia.

    abstract::This study was undertaken to characterize bile acid metabolism in hereditary forms of hypertriglyceridemia. Ten hypertriglyceridemic patients (type IV phenotype) with familial combined hyperlipidemia and 7 patients with monogenic familial hypertriglyceridemia (FHTG) were compared with 18 healthy controls; all subjects...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.84.15.5434

    authors: Angelin B,Hershon KS,Brunzell JD

    更新日期:1987-08-01 00:00:00

  • Nematic twist-bend phase in an external field.

    abstract::The response of the nematic twist-bend ([Formula: see text]) phase to an applied field can provide important insight into the structure of this liquid and may bring us closer to understanding mechanisms generating mirror symmetry breaking in a fluid of achiral molecules. Here we investigate theoretically how an extern...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1721786115

    authors: Pająk G,Longa L,Chrzanowska A

    更新日期:2018-10-30 00:00:00

  • Monarch butterflies (Danaus plexippus L.) use a magnetic compass for navigation.

    abstract::Fall migratory monarch butterflies, tested for their directional responses to magnetic cues under three conditions, amagnetic, normal, and reversed magnetic fields, showed three distinct patterns. In the absence of a magnetic field, monarchs lacked directionality as a group. In the normal magnetic field, monarchs orie...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章,收录出版

    doi:10.1073/pnas.96.24.13845

    authors: Etheredge JA,Perez SM,Taylor OR,Jander R

    更新日期:1999-11-23 00:00:00

  • Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites.

    abstract::The planarity of peptide bonds is an assumption that underlies decades of theoretical modeling of proteins. Peptide bonds strongly deviating from planarity are considered very rare features of protein structure that occur for functional reasons. Here, empirical analyses of atomic-resolution protein structures reveal t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1107115108

    authors: Berkholz DS,Driggers CM,Shapovalov MV,Dunbrack RL Jr,Karplus PA

    更新日期:2012-01-10 00:00:00

  • Arginine-deprivation-induced oxidative damage sterilizes Mycobacterium tuberculosis.

    abstract::Reactive oxygen species (ROS)-mediated oxidative stress and DNA damage have recently been recognized as contributing to the efficacy of most bactericidal antibiotics, irrespective of their primary macromolecular targets. Inhibitors of targets involved in both combating oxidative stress as well as being required for in...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1808874115

    authors: Tiwari S,van Tonder AJ,Vilchèze C,Mendes V,Thomas SE,Malek A,Chen B,Chen M,Kim J,Blundell TL,Parkhill J,Weinrick B,Berney M,Jacobs WR Jr

    更新日期:2018-09-25 00:00:00

  • C-type lectin receptor LSECtin-mediated apoptotic cell clearance by macrophages directs intestinal repair in experimental colitis.

    abstract::Epithelial barrier disruption is a major cause of inflammatory bowel disease (IBD); however, the cellular and molecular regulation of intestinal epithelial homeostasis remains largely undefined. Here, we show that the C-type lectin receptor LSECtin (Clec4g) on macrophages is required for protection against dextran sul...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1804094115

    authors: Yang Z,Li Q,Wang X,Jiang X,Zhao D,Lin X,He F,Tang L

    更新日期:2018-10-23 00:00:00

  • Combined molecular dynamics and neural network method for predicting protein antifreeze activity.

    abstract::Antifreeze proteins (AFPs) are a diverse class of proteins that depress the kinetically observable freezing point of water. AFPs have been of scientific interest for decades, but the lack of an accurate model for predicting AFP activity has hindered the logical design of novel antifreeze systems. To address this, we p...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1814945115

    authors: Kozuch DJ,Stillinger FH,Debenedetti PG

    更新日期:2018-12-26 00:00:00

  • Dynamic neural architecture for social knowledge retrieval.

    abstract::Social behavior is often shaped by the rich storehouse of biographical information that we hold for other people. In our daily life, we rapidly and flexibly retrieve a host of biographical details about individuals in our social network, which often guide our decisions as we navigate complex social interactions. Even ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1621234114

    authors: Wang Y,Collins JA,Koski J,Nugiel T,Metoki A,Olson IR

    更新日期:2017-04-18 00:00:00

  • An NQO1- and PARP-1-mediated cell death pathway induced in non-small-cell lung cancer cells by beta-lapachone.

    abstract::Lung cancer is the number one cause of cancer-related deaths in the world. Patients treated with current chemotherapies for non-small-cell lung cancers (NSCLCs) have a survival rate of approximately 15% after 5 years. Novel approaches are needed to treat this disease. We show elevated NAD(P)H:quinone oxidoreductase-1 ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0702176104

    authors: Bey EA,Bentle MS,Reinicke KE,Dong Y,Yang CR,Girard L,Minna JD,Bornmann WG,Gao J,Boothman DA

    更新日期:2007-07-10 00:00:00

  • Stratification of reactivity determines nitrate removal in groundwater.

    abstract::Biogeochemical reactions occur unevenly in space and time, but this heterogeneity is often simplified as a linear average due to sparse data, especially in subsurface environments where access is limited. For example, little is known about the spatial variability of groundwater denitrification, an important process in...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1816892116

    authors: Kolbe T,de Dreuzy JR,Abbott BW,Aquilina L,Babey T,Green CT,Fleckenstein JH,Labasque T,Laverman AM,Marçais J,Peiffer S,Thomas Z,Pinay G

    更新日期:2019-02-12 00:00:00

  • Long-term change in the organization of inventive activity.

    abstract::Relying on a quantitative analysis of the patenting and assignment behavior of inventors, we highlight the evolution of institutions that encouraged trade in technology and a growing division of labor between those who invented new technologies and those who exploited them commercially over the nineteenth and early-tw...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.23.12686

    authors: Lamoreaux NR,Sokoloff KL

    更新日期:1996-11-12 00:00:00

  • Dopa decarboxylase activity of the living human brain.

    abstract::Monoaminergic neurons use dopa decarboxylase (DDC; aromatic-L-amino-acid carboxy-lyase, EC 4.1.1.28) to form dopamine from L-3,4-dihydroxyphenylalanine (L-dopa). We measured regional dopa decarboxylase activity in brains of six healthy volunteers with 6-[18F]fluoro-L-dopa and positron emission tomography. We calculate...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.7.2721

    authors: Gjedde A,Reith J,Dyve S,Léger G,Guttman M,Diksic M,Evans A,Kuwabara H

    更新日期:1991-04-01 00:00:00

  • Phosphorylation of tyrosine residues of calmodulin in Rous sarcoma virus-transformed cells.

    abstract::Calmodulin, a wide-spread eukaryotic Ca2+-binding protein, was phosphorylated at its tyrosine residues in Rous sarcoma virus (RSV)-transformed chicken and rat cells but not in normal chicken embryo fibroblasts. In contrast, serine and threonine phosphorylation of calmodulin was found to occur in both normal and virus-...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.12.4190

    authors: Fukami Y,Nakamura T,Nakayama A,Kanehisa T

    更新日期:1986-06-01 00:00:00

  • Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes.

    abstract::The human proteome contains a plethora of short linear motifs (SLiMs) that serve as binding interfaces for modular protein domains. Such interactions are crucial for signaling and other cellular processes, but are difficult to detect because of their low to moderate affinities. Here we developed a dedicated approach, ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1312296111

    authors: Ivarsson Y,Arnold R,McLaughlin M,Nim S,Joshi R,Ray D,Liu B,Teyra J,Pawson T,Moffat J,Li SS,Sidhu SS,Kim PM

    更新日期:2014-02-18 00:00:00

  • An experimental test for lineage-specific position effects on alcohol dehydrogenase (Adh) genes in Drosophila.

    abstract::Independent transgene insertions differ in expression based on their location in the genome; these position effects are of interest because they reflect the influence of genome organization on gene regulation. Position effects also represent potentially insurmountable obstacles to the rigorous functional comparison of...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.26.15513

    authors: Siegal ML,Hartl DL

    更新日期:1998-12-22 00:00:00

  • The impact of climate change on smallholder and subsistence agriculture.

    abstract::Some of the most important impacts of global climate change will be felt among the populations, predominantly in developing countries, referred to as "subsistence" or "smallholder" farmers. Their vulnerability to climate change comes both from being predominantly located in the tropics, and from various socioeconomic,...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章,评审

    doi:10.1073/pnas.0701855104

    authors: Morton JF

    更新日期:2007-12-11 00:00:00

  • Membrane curvature underlies actin reorganization in response to nanoscale surface topography.

    abstract::Surface topography profoundly influences cell adhesion, differentiation, and stem cell fate control. Numerous studies using a variety of materials demonstrate that nanoscale topographies change the intracellular organization of actin cytoskeleton and therefore a broad range of cellular dynamics in live cells. However,...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1910166116

    authors: Lou HY,Zhao W,Li X,Duan L,Powers A,Akamatsu M,Santoro F,McGuire AF,Cui Y,Drubin DG,Cui B

    更新日期:2019-11-12 00:00:00

  • L596-W733 bond between the start of the S4-S5 linker and the TRP box stabilizes the closed state of TRPV4 channel.

    abstract::Unlike other cation channels, each subunit of most transient receptor potential (TRP) channels has an additional TRP-domain helix with an invariant tryptophan immediately trailing the gate-bearing S6. Recent cryo-electron microscopy of TRP vanilloid subfamily, member 1 structures revealed that this domain is a five-tu...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1502366112

    authors: Teng J,Loukin SH,Anishkin A,Kung C

    更新日期:2015-03-17 00:00:00

  • African trypanosomes expressing multiple VSGs are rapidly eliminated by the host immune system.

    abstract::Trypanosoma brucei parasites successfully evade the host immune system by periodically switching the dense coat of variant surface glycoprotein (VSG) at the cell surface. Each parasite expresses VSGs in a monoallelic fashion that is tightly regulated. The consequences of exposing multiple VSGs during an infection, in ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1905120116

    authors: Aresta-Branco F,Sanches-Vaz M,Bento F,Rodrigues JA,Figueiredo LM

    更新日期:2019-10-08 00:00:00

  • Related cell-surface antigens expressed with positional specificity in Drosophila imaginal discs.

    abstract::We have isolated three classes of monoclonal antibodies against Drosophila cell-surface antigens that are expressed with positional specificity in imaginal discs. Comparison of immunofluorescence patterns with the wing-disc fate map reveals that expression of the antigens is not directly related to the specific type o...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.81.23.7485

    authors: Brower DL,Wilcox M,Piovant M,Smith RJ,Reger LA

    更新日期:1984-12-01 00:00:00

  • Structure of canine pulmonary surfactant apoprotein: cDNA and complete amino acid sequence.

    abstract::The apoproteins of pulmonary surfactant (PSAP) are thought to be critical for normal surfactant function. They bind to surfactant phospholipids and enhance their ability to form surface films in vitro. These acidic glycoproteins have monomeric molecular weights of 36,000, 32,000, and 28,000 (PSAP-36, -32, and -28). Ea...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.82.19.6379

    authors: Benson B,Hawgood S,Schilling J,Clements J,Damm D,Cordell B,White RT

    更新日期:1985-10-01 00:00:00

  • Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily.

    abstract::Insight regarding how diverse enzymatic functions and reactions have evolved from ancestral scaffolds is fundamental to understanding chemical and evolutionary biology, and for the exploitation of enzymes for biotechnology. We undertook an extensive computational analysis using a unique and comprehensive combination o...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1706849114

    authors: Akiva E,Copp JN,Tokuriki N,Babbitt PC

    更新日期:2017-11-07 00:00:00

  • Chaperone-facilitated copper binding is a property common to several classes of familial amyotrophic lateral sclerosis-linked superoxide dismutase mutants.

    abstract::Mutations in Cu, Zn superoxide dismutase (SOD1) cause the neurodegenerative disease familial amyotrophic lateral sclerosis from an as-yet-unidentified toxic property(ies). Analysis in Saccharomyces cerevisiae of a broad range of human familial amyotrophic lateral sclerosis-linked SOD1 mutants (A4V, G37R, G41D, H46R, H...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.11.6361

    authors: Corson LB,Strain JJ,Culotta VC,Cleveland DW

    更新日期:1998-05-26 00:00:00

  • Urokinase-type plasminogen activator is effective in fibrin clearance in the absence of its receptor or tissue-type plasminogen activator.

    abstract::The availability of gene-targeted mice deficient in the urokinase-type plasminogen activator (uPA), urokinase receptor (uPAR), tissue-type plasminogen activator (tPA), and plasminogen permits a critical, genetic-based analysis of the physiological and pathological roles of the two mammalian plasminogen activators. We ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.12.5899

    authors: Bugge TH,Flick MJ,Danton MJ,Daugherty CC,Romer J,Dano K,Carmeliet P,Collen D,Degen JL

    更新日期:1996-06-11 00:00:00

  • Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes.

    abstract::For most intracellular structures with larger than molecular dimensions, little is known about the connection between underlying molecular activities and higher order organization such as size and shape. Here, we show that both the size and shape of the amphibian oocyte nucleolus ultimately arise because nucleoli beha...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1017150108

    authors: Brangwynne CP,Mitchison TJ,Hyman AA

    更新日期:2011-03-15 00:00:00

  • Unexpected central role of the androgen receptor in the spontaneous regeneration of myelin.

    abstract::Lost myelin can be replaced after injury or during demyelinating diseases in a regenerative process called remyelination. In the central nervous system (CNS), the myelin sheaths, which protect axons and allow the fast propagation of electrical impulses, are produced by oligodendrocytes. The abundance and widespread di...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1614826113

    authors: Bielecki B,Mattern C,Ghoumari AM,Javaid S,Smietanka K,Abi Ghanem C,Mhaouty-Kodja S,Ghandour MS,Baulieu EE,Franklin RJ,Schumacher M,Traiffort E

    更新日期:2016-12-20 00:00:00

  • Development and application of a suite of polysaccharide-degrading enzymes for analyzing plant cell walls.

    abstract::To facilitate analysis of plant cell wall polysaccharide structure and composition, we cloned 74 genes encoding polysaccharide-degrading enzymes from Aspergillus nidulans, Aspergillus fumigatus, and Neurospora crassa and expressed the genes as secreted proteins with C-terminal Myc and 6x His tags. Most of the recombin...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0604632103

    authors: Bauer S,Vasu P,Persson S,Mort AJ,Somerville CR

    更新日期:2006-07-25 00:00:00