Nature Chemical Biology
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Erratum: The role of dynamic conformational ensembles in biomolecular recognition
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Nature Chemical Biology 5, 954 (2009). doi:10.1038/nchembio1209-954d
Author: David D Boehr, Ruth Nussinov & Peter E Wright (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 14, 2009 Category: Biology Authors: David D BoehrRuth NussinovPeter E Wright Tags: Erratum Source Type: journals
Erratum: Targeting proteins for degradation
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Nature Chemical Biology 5, 954 (2009). doi:10.1038/nchembio1209-954c
Author: Erin K Schrader, Kristine G Harstad & Andreas Matouschek (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 14, 2009 Category: Biology Authors: Erin K SchraderKristine G HarstadAndreas Matouschek Tags: Erratum Source Type: journals
Erratum: S1P1 signaling just keeps going and going and going...
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Nature Chemical Biology 5, 954 (2009). doi:10.1038/nchembio1209-954b
Author: Stuart Cahalan & Hugh Rosen (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 14, 2009 Category: Biology Authors: Stuart CahalanHugh Rosen Tags: Erratum Source Type: journals
Corrigendum: Persistent signaling induced by FTY720-phosphate is mediated by internalized S1P1 receptors
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Nature Chemical Biology 5, 954 (2009). doi:10.1038/nchembio1209-954a
Author: Florian Mullershausen, Frédéric Zecri, Cihan Cetin, Andreas Billich, Danilo Guerini & Klaus Seuwen (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 14, 2009 Category: Biology Authors: Florian MullershausenFrédéric ZecriCihan CetinAndreas BillichDanilo GueriniKlaus Seuwen Tags: Corrigendum Source Type: journals
Research highlights
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Nature Chemical Biology 5, 876 (2009). doi:10.1038/nchembio.270 (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 14, 2009 Category: Biology Tags: News and Views Source Type: journals
On the mechanism of iron sensing by IRP2: new players, new paradigms
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y Kaplan
Two iron regulatory proteins (IRP1 and IRP2) regulate translation and/or stability of mRNAs encoding proteins required for iron storage, acquisition and utilization. Rather than IRP2 directly sensing iron concentrations, iron has been shown to regulate the level of the SKP1-CUL1-FBXL5 E3 ubiquitin ligase protein complex, which is responsible for IRP2 degradation. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 14, 2009 Category: Biology Authors: Naoko Takahashi-MakiseDiane McVey WardJerry Kaplan Tags: News and Views Source Type: journals
PKR and the ribosome compete for mRNA
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lacqua
The RNA-activated protein kinase PKR inhibits translation initiation by sensing long viral double-stranded RNA. A new report indicates that PKR is also activated by a cellular mRNA, but only when ribosomes are not initiating translation. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 14, 2009 Category: Biology Authors: Rebecca ToroneyPhilip C Bevilacqua Tags: News and Views Source Type: journals
Genomic variations on a CoA biosynthetic theme
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Nature Chemical Biology 5, 871 (2009). doi:10.1038/nchembio.267
Author: Andrei L Osterman
A unique heterotrimeric assembly of individually inactive paralogs, two of which are also involved in regulating phosphatase activity, creates one of the key enzymes of coenzyme A biosynthesis in yeast, pointing to the possibility of a previously undescribed cross-talk between metabolic and signaling pathways. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 14, 2009 Category: Biology Authors: Andrei L Osterman Tags: News and Views Source Type: journals
Deciphering bacterial language
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Nature Chemical Biology 5, 870 (2009). doi:10.1038/nchembio.263
Author: Vanessa Sperandio
Vibrio cholerae produces cholera autoinducer-1 (CAI-1), a signaling molecule previously believed to be synthesized by the CqsA enzyme. Here it is shown that CqsA does not directly synthesize CAI-1; instead, it synthesizes amino-CAI-1, which is then converted into CAI-1 in a CqsA-independent manner. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 14, 2009 Category: Biology Authors: Vanessa Sperandio Tags: News and Views Source Type: journals
Nitrate and nitrite in biology, nutrition and therapeutics
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hapiro, Andrey V Kozlov, Jack R Lancaster, David J Lefer, Kenneth McColl, Kenneth McCurry, Rakesh P Patel, Joel Petersson, Tienush Rassaf, Valentin P Reutov, George B Richter-Addo, Alan Schechter, Sruti Shiva, Koichiro Tsuchiya, Ernst E van Faassen, Andrew J Webb, Brian S Zuckerbraun, Jay L Zweier & Eddie Weitzberg
Inorganic nitrate and nitrite from endogenous or dietary sources are metabolized in vivo to nitric oxide (NO) and other bioactive nitrogen oxides. The nitrate-nitrite-NO pathway is emerging as an important mediator of blood flow regulation, cell signaling, energetics and tissue responses to hypoxia. The late...
Source: Nature Chemical Biology - November 14, 2009 Category: Biology Authors: Jon O LundbergMark T GladwinAmrita AhluwaliaNigel BenjaminNathan S BryanAnthony ButlerPedro CabralesAngela FagoMartin FeelischPeter C FordBruce A FreemanMichael FrenneauxJoel FriedmanMalte KelmChristopher G KevilDaniel B Kim-ShapiroAndrey V KozlovJack R L Tags: Meeting Report Source Type: journals
Come together
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Nature Chemical Biology 5, 863 (2009). doi:10.1038/nchembio.272
The third Nature Chemical Biology symposium brought together nearly 200 scientists to explore the frontiers of chemical biology and drug discovery. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 14, 2009 Category: Biology Tags: Editorial Source Type: journals
In this issue
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Nature Chemical Biology 5, v (2009). doi:10.1038/nchembio.269 (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 14, 2009 Category: Biology Tags: In This Issue Source Type: journals
Translating metabolic exchange with imaging mass spectrometry
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Dorrestein
Metabolic exchange between an organism and the environment, including interactions with neighboring organisms, is important for processes of organismal development. Here we develop and use thin-layer agar natural product MALDI-TOF imaging mass spectrometry of intact bacterial colonies grown on top of the MALDI target plate to study an interaction between two species of bacteria and provide direct evidence that Bacillus subtilis silences the defensive arsenal of Streptomyces coelicolor. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 8, 2009 Category: Biology Authors: Yu-Liang YangYuquan XuPaul StraightPieter C Dorrestein Tags: Brief Communication Source Type: journals
An artificial di-iron oxo-protein with phenol oxidase activity
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p; Angela Lombardi
Here we report the de novo design and NMR structure of a four-helical bundle di-iron protein with phenol oxidase activity. The introduction of the cofactor-binding and phenol-binding sites required the incorporation of residues that were detrimental to the free energy of folding of the protein. Sufficient stability was, however, obtained by optimizing the sequence of a loop distant from the active site. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 8, 2009 Category: Biology Authors: Marina FaiellaConcetta AndreozziRafael Torres Martin de RosalesVincenzo PavoneOrnella MaglioFlavia NastriWilliam F DeGradoAngela Lombardi Tags: Brief Communication Source Type: journals
A synergistic small-molecule combination directly eradicates diverse prion strain structures
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amp; James Shorter (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 1, 2009 Category: Biology Authors: Blake E RobertsMartin L DuennwaldHuan WangChan ChungNicholas P LopreiatoElizabeth A SweenyM Noelle KnightJames Shorter Tags: Article Source Type: journals
Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem
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gchong You (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 1, 2009 Category: Biology Authors: Hao SongStephen PayneMeagan GrayLingchong You Tags: Article Source Type: journals
Moonlighting proteins Hal3 and Vhs3 form a heteromeric PPCDC with Ykl088w in yeast CoA biosynthesis
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Joaquín Ariño (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - November 1, 2009 Category: Biology Authors: Amparo RuizAsier GonzálezIvan MuñozRaquel SerranoJ Albert AbrieErick StraussJoaquín Ariño Tags: Article Source Type: journals
Natural amino acids do not require their native tRNAs for efficient selection by the ribosome
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rginia W Cornish (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 25, 2009 Category: Biology Authors: Philip R EffraimJiangning WangMichael T EnglanderJosh AvinsThomas S LeyhRuben L GonzalezVirginia W Cornish Tags: Article Source Type: journals
Small-molecule inhibitors target Escherichia coli amyloid biogenesis and biofilm formation
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man & Scott J Hultgren (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 25, 2009 Category: Biology Authors: Lynette CegelskiJerome S PinknerNeal D HammerCorinne K CusumanoChia S HungErik ChorellVeronica ÅbergJennifer N WalkerPatrick C SeedFredrik AlmqvistMatthew R ChapmanScott J Hultgren Tags: Article Source Type: journals
Diverse backbone-cyclized peptides via codon reprogramming
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We report a methodology for the ribosomal synthesis of backbone-cyclized peptides involving genetic code reprogramming to introduce one or more nonproteinogenic amino acids. Expression of linear peptides bearing a cysteine-proline dipeptide sequence followed by glycolic acid results in self-rearrangement to a C-terminal diketopiperadine-thioester, which non-enzymatically generates a cyclized peptide. We demonstrate the ribosomal synthesis of several naturally occurring backbone-cyclized peptides and a library based on a bicyclic scaffold, and we identify bioactive sequences by screening and deconvolution. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 25, 2009 Category: Biology Authors: Takashi KawakamiAtsushi OhtaMasaki OhuchiHiroshi AshigaiHiroshi MurakamiHiroaki Suga Tags: Brief Communication Source Type: journals
Research highlights
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Nature Chemical Biology 5, 786 (2009). doi:10.1038/nchembio.253 (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 20, 2009 Category: Biology Tags: News and Views Source Type: journals
Slow growth leads to a switch
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Nature Chemical Biology 5, 784 (2009). doi:10.1038/nchembio.248
Author: Keith Shearwin
Synthetic biologists aim to rationally design and construct useful biological circuits. However, perturbation of host cell physiology, through the very process of turning on an artificial circuit, can give rise to unexpected emergent behaviors, such as bistability. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 20, 2009 Category: Biology Authors: Keith Shearwin Tags: News and Views Source Type: journals
The physical chemistry of membrane curvature
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Nature Chemical Biology 5, 783 (2009). doi:10.1038/nchembio.247
Author: Jay T Groves
Membrane curvature sensing by amphipathic helices is an emergent property of the ensemble of molecules and membrane sites. New data suggest that individual molecules do not experience stronger binding to curved membranes. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 20, 2009 Category: Biology Authors: Jay T Groves Tags: News and Views Source Type: journals
Locking out viral replication
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Varani
Few antimicrobial drugs function by directly targeting RNA. A small molecule that binds the hepatitis C viral genome by 'locking' in a particular RNA conformation to inhibit viral protein production suggests a new paradigm for drug design. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 20, 2009 Category: Biology Authors: Darren W BegleyGabriele Varani Tags: News and Views Source Type: journals
The nanny model for IDPs
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We describe here a model wherein a group of 'nanny' proteins function to protect newly synthesized IDPs from degradation by default, thereby insuring their maturation into important regulatory molecules. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 20, 2009 Category: Biology Authors: Peter TsvetkovNina ReuvenYosef Shaul Tags: Commentary Source Type: journals
Post-reductionist protein science, or putting Humpty Dumpty back together again
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henson
In their native environments, proteins perform their biological roles in highly concentrated viscous solutions and in complex networks with numerous partners. Yet for many years, the normal practice has been to purify a protein of interest in order to characterize its structural and functional properties. In this Commentary, we discuss how protein scientists are now tackling the theoretical and methodological challenges of studying proteins in their physiological context. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 20, 2009 Category: Biology Authors: Lila M GieraschAnne Gershenson Tags: Commentary Source Type: journals
Eyes wide open
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Nature Chemical Biology 5, 773 (2009). doi:10.1038/nchembio.258
Understanding how proteins function in isolation and in their native context requires a merging of molecular-level techniques that explore the interplay of protein structure and dynamics. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 20, 2009 Category: Biology Tags: Editorial Source Type: journals
In this issue
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Nature Chemical Biology 5, v (2009). doi:10.1038/nchembio.254 (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 20, 2009 Category: Biology Tags: In This Issue Source Type: journals
Targeting proteins for degradation
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touschek (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 18, 2009 Category: Biology Authors: Erin K SchraderKristine G HarstadAndreas Matouschek Tags: Review Source Type: journals
NMR spectroscopy brings invisible protein states into focus
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E Kay (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 18, 2009 Category: Biology Authors: Andrew J BaldwinLewis E Kay Tags: Review Source Type: journals
Computer-aided design of functional protein interactions
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rtemme (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 18, 2009 Category: Biology Authors: Daniel J MandellTanja Kortemme Tags: Review Source Type: journals
Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome
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nt Croquette (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 18, 2009 Category: Biology Authors: Maria ManosasMichelle M SpieringZhihao ZhuangStephen J BenkovicVincent Croquette Tags: Article Source Type: journals
The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA
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& Bonnie L Bassler (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 18, 2009 Category: Biology Authors: Robert C KellyMegan E BolithoDouglas A HigginsWenyun LuWai-Leung NgPhilip D JeffreyJoshua D RabinowitzMartin F SemmelhackFrederick M HughsonBonnie L Bassler Tags: Article Source Type: journals
LC/MS analysis of cellular RNA reveals NAD-linked RNA
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David R Liu
We developed a general method to detect cellular small molecule–RNA conjugates that does not rely on the reactivity of the small molecule. This technique revealed NAD-linked RNA in Escherichia coli and Streptomyces venezuelae. Subsequent characterization showed that NAD is a 5′ modification of RNA, cannot be installed in vitro through aberrant transcriptional initiation, is only found among smaller cellular RNAs and is present at a surprisingly high abundance of ∼3,000 copies per cell. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 11, 2009 Category: Biology Authors: Y Grace ChenWalter E KowtoniukIsha AgarwalYinghua ShenDavid R Liu Tags: Brief Communication Source Type: journals
The role of dynamic conformational ensembles in biomolecular recognition
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E Wright (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 9, 2009 Category: Biology Authors: David D BoehrRuth NussinovPeter E Wright Tags: Perspective Source Type: journals
Dynamic refolding of IFN-γ mRNA enables it to function as PKR activator and translation template
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Dynamic refolding of IFN-γ mRNA enables it to function as PKR activator and translation template
Nature Chemical Biology 5, 896 (2009). doi:10.1038/nchembio.234
Authors: Smadar Cohen-Chalamish, Anat Hasson, Dahlia Weinberg, Lise Sarah Namer, Yona Banai, Farhat Osman & Raymond Kaempfer (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 4, 2009 Category: Biology Authors: Smadar Cohen-ChalamishAnat HassonDahlia WeinbergLise Sarah NamerYona BanaiFarhat OsmanRaymond Kaempfer Tags: Article Source Type: journals
Emergent bistability by a growth-modulating positive feedback circuit
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hong You (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - October 3, 2009 Category: Biology Authors: Cheemeng TanPhilippe MarguetLingchong You Tags: Article Source Type: journals
Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting
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tta & Eric D Brown (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - September 26, 2009 Category: Biology Authors: Ranjana PathaniaSoumaya ZlitniCourtney BarkerRahul DasDavid A GerritsmaJulie LebertEmilia AwuahGiuseppe MelaciniFred A CaprettaEric D Brown Tags: Article Source Type: journals
Erratum: Design, synthesis and selection of DNA-encoded small-molecule libraries
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Nature Chemical Biology 5, 772 (2009). doi:10.1038/nchembio1009-772
Author: Matthew A Clark, Raksha A Acharya, Christopher C Arico-Muendel, Svetlana L Belyanskaya, Dennis R Benjamin, Neil R Carlson, Paolo A Centrella, Cynthia H Chiu, Steffen P Creaser, John W Cuozzo, Christopher P Davie, Yun Ding, G Joseph Franklin, Kurt D Franzen, Malcolm L Gefter, Steven P Hale, Nils J V Hansen, David I Israel, Jinwei Jiang, Malcolm J Kavarana, Michael S Kelley, Christopher S Kollmann, Fan Li, Kenneth Lind, Sibongile Mataruse, Patricia F Medeiros, Jeffrey A Messer, Paul Myers, Heather O'Keefe, Matthew C Oliff, Cecil E Rise, Alexander ...
Source: Nature Chemical Biology - September 24, 2009 Category: Biology Authors: Matthew A ClarkRaksha A AcharyaChristopher C Arico-MuendelSvetlana L BelyanskayaDennis R BenjaminNeil R CarlsonPaolo A CentrellaCynthia H ChiuSteffen P CreaserJohn W CuozzoChristopher P DavieYun DingG Joseph FranklinKurt D FranzenMalcolm L GefterSteven P Tags: Erratum Source Type: journals
Research highlights
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Nature Chemical Biology 5, 712 (2009). doi:10.1038/nchembio.230 (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - September 24, 2009 Category: Biology Tags: News and Views Source Type: journals
DNA-catalyzed hydrolysis of DNA phosphodiesters
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Gates
Hydrolysis of the phosphodiester linkages in DNA is a notoriously difficult reaction. Deoxyribozymes that use Zn2+ and Mn2+ ions to accelerate this reaction by a factor of one hundred million (or more) have been identified and characterized. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - September 24, 2009 Category: Biology Authors: Mostafa I FekryKent S Gates Tags: News and Views Source Type: journals
Chemo-metabolic regulation of immune responses by Tregs
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Sitia
Chemo-metabolic processes such as redox remodeling and amino acid availability act as immunity rheostats, revealing a new mechanism regulating intercellular cross-talk between dendritic cells, regulatory T lymphocytes and effector T lymphocytes. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - September 24, 2009 Category: Biology Authors: Anna RubartelliRoberto Sitia Tags: News and Views Source Type: journals
When two keys fit one lock, surprises follow
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Nature Chemical Biology 5, 707 (2009). doi:10.1038/nchembio.225
Author: Michael Rosenblatt
Parathyroid hormone (PTH) and PTH-related protein activate the same receptor but can produce divergent effects. Reports now describe two active conformations for the PTH receptor, one of which moves intracellularly—complexed with hormone and G protein—to produce a continued cAMP signal. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - September 24, 2009 Category: Biology Authors: Michael Rosenblatt Tags: News and Views Source Type: journals
Cells' senses and sensibilities
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ulsson (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - September 24, 2009 Category: Biology Authors: Shay TalJohan Paulsson Tags: Book Review Source Type: journals
Not all quiet on the noise front
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nter & Hana El-Samad (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - September 24, 2009 Category: Biology Authors: Emma McCullaghJustin FarlowChristopher FullerJuliet GirardJoanna Lipinski-KruszkaDan LuThomas NoriegaGeoffrey RollinsRussell SpitzerMichael TodhunterHana El-Samad Tags: Commentary Source Type: journals
Assigning responsibility and credit
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Nature Chemical Biology 5, 697 (2009). doi:10.1038/nchembio.f.13
New policies refine the responsibilities of authors and require author contribution statements in Nature Chemical Biology research papers. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - September 24, 2009 Category: Biology Tags: Editorial Source Type: journals
In this issue
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Nature Chemical Biology 5, v (2009). doi:10.1038/nchembio.231 (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - September 24, 2009 Category: Biology Tags: In This Issue Source Type: journals
Corrigendum: A 21st century revisionist's view at a turning point in enzymology
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Nature Chemical Biology 5, 696 (2009). doi:10.1038/nchembio0909-696c
Author: Zachary D Nagel & Judith P Klinman (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - September 22, 2009 Category: Biology Authors: Zachary D NagelJudith P Klinman Tags: Corrigendum Source Type: journals
Corrigendum: Interactive exploration of chemical space with Scaffold Hunter
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Nature Chemical Biology 5, 696 (2009). doi:10.1038/nchembio0909-696b
Author: Stefan Wetzel, Karsten Klein, Steffen Renner, Daniel Rauh, Tudor I Oprea, Petra Mutzel & Herbert Waldmann (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - September 22, 2009 Category: Biology Authors: Stefan WetzelKarsten KleinSteffen RennerDaniel RauhTudor I OpreaPetra MutzelHerbert Waldmann Tags: Corrigendum Source Type: journals
Corrigendum: Chromatin-level regulation of biosynthetic gene clusters
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Nature Chemical Biology 5, 696 (2009). doi:10.1038/nchembio0909-696a
Author: Jin Woo Bok, Yi-Ming Chiang, Edyta Szewczyk, Yazmid Reyes-Dominguez, Ashley D Davidson, James F Sanchez, Hsien-Chun Lo, Kenji Watanabe, Joseph Strauss, Berl R Oakley, Clay C C Wang & Nancy P Keller (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - September 22, 2009 Category: Biology Authors: Jin Woo BokYi-Ming ChiangEdyta SzewczykYazmid Reyes-DominguezAshley D DavidsonJames F SanchezHsien-Chun LoKenji WatanabeJoseph StraussBerl R OakleyClay C C WangNancy P Keller Tags: Corrigendum Source Type: journals
