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1. In Silico Evolution of Biochemical Log-Response

Author:
Hemery, Mathieu; François, Paul
Source:
TheJournal of physical chemistry 2019 v.123 no.10 pp. 2235-2243
ISSN:
1520-5207
Subject:
phosphorylation,   etc   ; algorithms; chemotaxis; ligands;     Show all 4 Subjects
Abstract:
... Numerous biological systems are known to harbor a form of logarithmic behavior, from Weber’s law to bacterial chemotaxis. Such a log-response allows for sensitivity to small relative variations of biochemical inputs over a large range of concentration values. Here we use a genetic algorithm to evolve biochemical networks displaying a logarithmic response. A quasi-perfect log-response implemented b ...
DOI:
10.1021/acs.jpcb.8b10974

2. The Phospho-Code Determining Circadian Feedback Loop Closure and Output in Neurospora

Author:
Wang, Bin; Kettenbach, Arminja N.; Zhou, Xiaoying; Loros, Jennifer J.; Dunlap, Jay C.
Source:
Molecular cell 2019 v.74 no.4 pp. 771-784.e3
ISSN:
1097-2765
Subject:
phosphorylation,   etc   ; Neurospora; cryptochromes; genes; transactivators;     Show all 5 Subjects
Abstract:
... In the negative feedback loop driving fungal and animal circadian oscillators, negative elements (FREQUENCY [FRQ], PERIODS [PERs], and CRYPTOCHROMES [CRYs]) are understood to inhibit their own expression, in part by promoting the phosphorylation of their heterodimeric transcriptional activators (e.g., White Collar-1 [WC-1]-WC-2 [White Collar complex; WCC] and BMAL1/Circadian Locomotor Output Cycle ...
DOI:
10.1016/j.molcel.2019.03.003

3. Cyclin-Specific Docking Mechanisms Reveal the Complexity of M-CDK Function in the Cell Cycle

Author:
Örd, Mihkel; Venta, Rainis; Möll, Kaidi; Valk, Ervin; Loog, Mart
Source:
Molecular cell 2019 v.75 no.1 pp. 76-89.e3
ISSN:
1097-2765
Subject:
phosphorylation,   etc   ; cyclin-dependent kinase; cyclins; mitosis; tyrosine;     Show all 5 Subjects
Abstract:
... Cyclin-dependent kinases (CDKs) coordinate hundreds of molecular events during the cell cycle. Multiple cyclins are involved, but the global role of cyclin-specific phosphorylation has remained unsolved. We uncovered a cyclin docking motif, LxF, that mediates binding of replication factor Cdc6 to mitotic cyclin. This interaction leads to phospho-adaptor Cks1-mediated inhibition of M-CDK to facilit ...
DOI:
10.1016/j.molcel.2019.04.026

4. DDQ-promoted C(sp3)H phosphorylation of cycloheptatriene

Author:
Wen, Chunxiao; Yu, Guodian; Ou, Yingcong; Wang, Xiaofeng; Zhang, Kun; Chen, Qian
Source:
Tetrahedron letters 2019 v.60 no.19 pp. 1345-1348
ISSN:
0040-4039
Subject:
phosphorylation,   etc   ; ambient temperature; moieties; organic compounds;     Show all 4 Subjects
Abstract:
... An efficient and convenient C(sp3)H phosphorylation has been achieved via the DDQ-promoted cross-dehydrogenative coupling between cycloheptatriene and P(O)H compounds at room temperature. This transformation provides a direct synthetic route to the construction of C(sp3)P bonds with good functional group compatibility, leading to the formation of cyclohepta-2,4,6-trien-1-ylphosphonates in up to 99 ...
DOI:
10.1016/j.tetlet.2019.04.021

5. Regioselective 5′-position phosphorylation of ribose and ribonucleosides: phosphate transfer in the activated pyrophosphate complex in the gas phase

Author:
HuThese authors contributed equally., Jun; Lei, Wen; Wang, Jiang; Chen, Hong-Yuan; Xu, Jing-Juan
Source:
Chemical communications 2019 v.55 no.3 pp. 310-313
ISSN:
1364-548X
Subject:
phosphorylation,   etc   ; gases; ionization; phosphates; regioselectivity; ribonucleosides; ribose;     Show all 7 Subjects
Abstract:
... Herein, we present a rapid, efficient and regioselective phosphorylation method at the 5′-position of unprotected ribose and ribonucleosides with pyrophosphate in the gas phase, which involves the formation of anionic complexes via electrospray ionization and collisional activation to induce phosphorylation within the complexes. ...
DOI:
10.1039/c8cc08510b

6. Protein Language: Post-Translational Modifications Talking to Each Other

Author:
Vu, Lam Dai; Gevaert, Kris; De Smet, Ive
Source:
Trends in plant science 2018 v.23 no.12 pp. 1068-1080
ISSN:
1360-1385
Subject:
phosphorylation,   etc   ; cell communication; sumoylation;     Show all 3 Subjects
Abstract:
... Post-translational modifications (PTMs) are at the heart of many cellular signaling events. Apart from a single regulatory PTM, there are also PTMs that function in orchestrated manners. Such PTM crosstalk usually serves as a fine-tuning mechanism to adjust cellular responses to the slightest changes in the environment. While PTM crosstalk has been studied in depth in various species; in plants, t ...
DOI:
10.1016/j.tplants.2018.09.004

7. Phosphorylation alters Bim‐mediated Mcl‐1 stabilization and priming

Author:
Conage‐Pough, Jason E.; Boise, Lawrence H.
Source:
TheFEBS journal 2018 v.285 no.14 pp. 2626-2640
ISSN:
1742-464X
Subject:
phosphorylation,   etc   ; apoptosis; mutation; proteins;     Show all 4 Subjects
Abstract:
... Mcl‐1 is a highly labile protein, subject to extensive post‐translational regulation. This distinguishes Mcl‐1 from other antiapoptotic proteins and necessitates further study to better understand how interactions with proapoptotic Bcl‐2 proteins affect its regulation. One such protein, Bim, is known to stabilize Mcl‐1, and Bim phosphorylation has been associated with increased Mcl‐1 binding. Cons ...
DOI:
10.1111/febs.14505

8. New reactions and processes for the efficient synthesis of a HCV NS5b prodrug

Author:
Orr, Robert K.; McCabe Dunn, Jamie M.; Nolting, Andrew; Hyde, Alan M.; Ashley, Eric R.; Leone, Joseph; Sirota, Eric; Jurica, Jon A.; Gibson, Andrew; Wise, Christopher; Oliver, Steven; Ruck, Rebecca T.
Source:
Green chemistry 2018 v.20 no.11 pp. 2519-2525
ISSN:
1463-9270
Subject:
phosphorylation,   etc   ; green chemistry; nucleosides;     Show all 3 Subjects
Abstract:
... Herein we describe the route scouting and process development efforts toward a green and sustainable synthesis of the HCV NS5b cyclic prodrug nucleoside (CPN) 1. Through the discovery and development of a crystallization-induced dynamic resolution and a novel chemo- and stereo-selective phosphorylation reaction, we eliminated costly chromatographies and protecting group manipulations utilized in t ...
DOI:
10.1039/c8gc00102b

9. Regulation of the Minichromosome Maintenance Protein 3 (MCM3) Chromatin Binding by the Prolyl Isomerase Pin1

Author:
Schumann, Michael; Malešević, Miroslav; Hinze, Erik; Mathea, Sebastian; Meleshin, Marat; Schutkowski, Mike; Haehnel, Wolfgang; Schiene-Fischer, Cordelia
Source:
Journal of molecular biology 2018 v.430 no.24 pp. 5169-5181
ISSN:
0022-2836
Subject:
phosphorylation,   etc   ; chromatin; humans; interphase; isomerases;     Show all 5 Subjects
Abstract:
... Human Pin1 is a peptidyl prolyl cis/trans isomerase with a unique preference for phosphorylated Ser/Thr-Pro substrate motifs.Here we report that MCM3 (minichromosome maintenance complex component 3) is a novel target of Pin1. MCM3 interacts directly with the WW domain of Pin1. Proline-directed phosphorylation of MCM3 at S112 and T722 are crucial for the interaction with Pin1. MCM3 as a subunit of ...
DOI:
10.1016/j.jmb.2018.10.002

10. A NAC Transcription Factor ZmNAC84 affects Pollen Development Through the Repression of ZmRbohH Expression in Maize

Author:
Yang, Qi; Zhang, Heping; Liu, Chen; Huang, Liping; Zhao, Lili; Zhang, Aying
Source:
Journal of plant biology 2018 v.61 no.6 pp. 366-373
ISSN:
1226-9239
Subject:
phosphorylation,   etc   ; corn; pollen; transcription factors;     Show all 4 Subjects
Abstract:
... The NAC proteins are plant-specific transcription factors and widely distributed in plants. The wide functions of NAC transcription factors were studied, but the roles of NAC in pollen development are largely unclear. Here, we found that ZmNAC84 played a vital role in maize pollen development. ZmRbohH showed high expression in pollen. ZmNAC84 inhibited the ZmRbohH expression by directly binding to ...
DOI:
10.1007/s12374-018-0227-z

11. To be or not to be: PP2A as a dual player in CNS functions, its role in neurodegeneration, and its interaction with brain insulin signaling

Author:
Javadpour, Pegah; Dargahi, Leila; Ahmadiani, Abolhassan; Ghasemi, Rasoul
Source:
Cellular and molecular life sciences 2019 v.76 no.12 pp. 2277-2297
ISSN:
1420-682X
Subject:
phosphorylation,   etc   ; brain; enzymes; insulin; neurodegenerative diseases; signal transduction;     Show all 6 Subjects
Abstract:
... Accumulating evidence has reached the consensus that the balance of phosphorylation state of signaling molecules is a pivotal point in the regulation of cell signaling. Therefore, characterizing elements (kinases–phosphatases) in the phosphorylation balance are at great importance. However, the role of phosphatase enzymes is less investigated than kinase enzymes. PP2A is a member of serine/threoni ...
DOI:
10.1007/s00018-019-03063-y

12. 5′-Morpholino modification of the sense strand of an siRNA makes it a more effective passenger

Author:
Kumar, Pawan; Parmar, Rubina G.; Brown, Christopher R.; Willoughby, Jennifer L. S.; Foster, Donald J.; Babu, I. Ramesh; Schofield, Sally; Jadhav, Vasant; Charisse, Klaus; Nair, Jayaprakash K.; Rajeev, Kallanthottathil G.; Maier, Martin A.; Egli, Martin; Manoharan, Muthiah
Source:
Chemical communications 2019 v.55 no.35 pp. 5139-5142
ISSN:
1364-548X
Subject:
phosphorylation,   etc   ; RNA interference; chemical compounds; small interfering RNA;     Show all 4 Subjects
Abstract:
... The 5′-monophosphate group plays an important role in strand selection during gene silencing mediated by small-interfering RNA. We show that blocking of 5′ phosphorylation of the sense strand by introducing a 5′-morpholino modification improves antisense strand selection and RNAi activity. The 5′-morpholino modification of the antisense strand triggers complete loss of activity. ...
DOI:
10.1039/c9cc00977a

13. FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates

Author:
Turco, Eleonora; Witt, Marie; Abert, Christine; Bock-Bierbaum, Tobias; Su, Ming-Yuan; Trapannone, Riccardo; Sztacho, Martin; Danieli, Alberto; Shi, Xiaoshan; Zaffagnini, Gabriele; Gamper, Annamaria; Schuschnig, Martina; Fracchiolla, Dorotea; Bernklau, Daniel; Romanov, Julia; Hartl, Markus; Hurley, James H.; Daumke, Oliver; Martens, Sascha
Source:
Molecular cell 2019 v.74 no.2 pp. 330-346.e11
ISSN:
1097-2765
Subject:
phosphorylation,   etc   ; autophagy; claws; condensates; crystal structure; separation; ubiquitin;     Show all 7 Subjects
Abstract:
... The autophagy cargo receptor p62 facilitates the condensation of misfolded, ubiquitin-positive proteins and their degradation by autophagy, but the molecular mechanism of p62 signaling to the core autophagy machinery is unclear. Here, we show that disordered residues 326–380 of p62 directly interact with the C-terminal region (CTR) of FIP200. Crystal structure determination shows that the FIP200 C ...
DOI:
10.1016/j.molcel.2019.01.035

14. Visualization and Analysis of Epiproteome Dynamics

Author:
Kaur, Sandeep; Baldi, Benedetta; Vuong, Jenny; O'Donoghue, Seán I.
Source:
Journal of molecular biology 2019 v.431 no.8 pp. 1519-1539
ISSN:
0022-2836
Subject:
phosphorylation,   etc   ; bioinformatics; data collection; post-translational modification; proteins;     Show all 5 Subjects
Abstract:
... The epiproteome describes the set of all post-translational modifications (PTMs) made to the proteins comprising a cell or organism. The extent of the epiproteome is still largely unknown; however, advances in experimental techniques are beginning to produce a deluge of data, tracking dynamic changes to the epiproteome in response to cellular stimuli. These data have potential to revolutionize our ...
DOI:
10.1016/j.jmb.2019.01.044

15. Single-site phosphorylation within the His-tag sequence attached to a recombinant protein

Author:
Singh, Himanshu; Verma, Deepshikha; Bardiaux, Benjamin
Source:
Analytical biochemistry 2019 v.570 pp. 62-64
ISSN:
0003-2697
Subject:
phosphorylation,   etc   ; enzymes; mass spectrometry; post-translational modification; recombinant proteins; serine;     Show all 6 Subjects
Abstract:
... We report the observation of single-site phosphorylation in a His-tag sequence N-terminally attached to a recombinant protein (UVI31+) in vitro. This modification was detected at position 23 at a serine residue of the His-tag sequence encoded by the vector pET28a. Furthermore, the phosphorylated tag sequence was found to be dephosphorylated by the action of alkaline phosphatases. The functional ac ...
DOI:
10.1016/j.ab.2019.02.001

16. Stressing out or stressing in: intracellular pathways for SAPK activation

Author:
Lee, Jongmin; Liu, Li; Levin, David E.
Source:
Current genetics 2019 v.65 no.2 pp. 417-421
ISSN:
0172-8083
Subject:
phosphorylation,   etc   ; DNA damage; arsenites; mitogen-activated protein kinase; yeasts;     Show all 5 Subjects
Abstract:
... Stress-activated MAP kinases (SAPKs) respond to a wide variety of stressors. In most cases, the pathways through which specific stress signals are transmitted to the SAPKs are not known. Our recent findings have begun to address two important and related questions. First, do various stresses activate a SAPK through common pathways initiated at the cell surface, or through alternative, intracellula ...
DOI:
10.1007/s00294-018-0898-5

17. Troponin I modulation of cardiac performance: Plasticity in the survival switch

Author:
Biesiadecki, Brandon J.; Westfall, Margaret V.
Source:
Archives of biochemistry and biophysics 2019 v.664 pp. 9-14
ISSN:
0003-9861
Subject:
phosphorylation,   etc   ; humans; models; plasticity; protein kinase C; sarcomeres; troponin I;     Show all 7 Subjects
Abstract:
... Signaling complexes targeting the myofilament are essential in modulating cardiac performance. A central target of this signaling is cardiac troponin I (cTnI) phosphorylation. This review focuses on cTnI phosphorylation as a model for myofilament signaling, discussing key gaps and future directions towards understanding complex myofilament modulation of cardiac performance. Human heart cTnI is pho ...
DOI:
10.1016/j.abb.2019.01.025

18. Eukaryotic Initiation Factor 4E (eIF4E) sequestration mediates 4E-BP1 response to rapamycin

Author:
Batool, Asiya; Majeed, Sheikh Tahir; Aashaq, Sabreena; Majeed, Rabiya; Shah, Ghazia; Nazir, Nadiem; Andrabi, Khurshid Iqbal
Source:
International journal of biological macromolecules 2019 v.125 pp. 651-659
ISSN:
0141-8130
Subject:
phosphorylation,   etc   ; glucose; messenger RNA; nutrients; rapamycin; translation (genetics);     Show all 6 Subjects
Abstract:
... The cap dependent translation initiation is a tightly controlled process of cooperative ternary complex formation by 4E-BP1, eIF4E and the 5′ cap of eukaryotic mRNA in response to environmental cues like glucose, nutrients and growth factor levels. Based on the well-described effects of mTORC1/rapamycin complex on 4E-BP1 phosphorylation/s, it is generally accepted that rapamycin is a global inhibi ...
DOI:
10.1016/j.ijbiomac.2018.12.102

19. PROTACs suppression of CDK4/6, crucial kinases for cell cycle regulation in cancer

Author:
Zhao, Bosheng; Burgess, Kevin
Source:
Chemical communications 2019 v.55 no.18 pp. 2704-2707
ISSN:
1364-548X
Subject:
phosphorylation,   etc   ; cell cycle checkpoints; chemical compounds; neoplasms; phosphotransferases (kinases); proteins;     Show all 6 Subjects
Abstract:
... PROTACs based on two selective, FDA approved, CDK4/6 inhibitors were formed. One of them, based on palbociclib, potently initiates degradation of these CDK proteins, and suppresses phosphorylation of retinoblastoma protein (Rb) leading to cell cycle arrest. These PROTACs are active at nanomolar concentrations, and appear to be the first for CDK4/6. ...
DOI:
10.1039/c9cc00163h

20. Analysis of RNA 5′ ends: Phosphate enumeration and cap characterization

Author:
Luciano, Daniel J.; Belasco, Joel G.
Source:
Methods 2019 v.155 pp. 3-9
ISSN:
1046-2023
Subject:
phosphorylation,   etc   ; NAD (coenzyme); Northern blotting; RNA; gel electrophoresis; phosphates;     Show all 6 Subjects
Abstract:
... The function and fate of cellular RNAs are often governed by the phosphorylation state at the 5′ end or the identity of whatever cap may be present there. Here we describe methods for examining these important 5′-terminal features on any cellular or synthetic RNA of interest that can be detected by Northern blotting. One such method, PABLO, is a splinted ligation assay that makes it possible to ac ...
DOI:
10.1016/j.ymeth.2018.10.023