December « 2011 « Molecular BioSystems Blog

Archive for December, 2011

Hot articles on xenobiotic screening, transcriptional regulatory networks, CD44 and more

23 Dec 2011

We’re just about to wrap up here for Christmas, but before we go we thought we’d give you some hot articles to keep you warm until the new year…

Using pathway modules as targets for assay development in xenobiotic screening
Richard S. Judson, Holly M. Mortensen, Imran Shah, Thomas B. Knudsen and Fathi Elloumi
DOI: 10.1039/C1MB05303E

Specific in situ discrimination of amyloid fibrils versus α-helical fibres by the fluorophore NIAD-4
Enrico Brandenburg, Hans v. Berlepsch and Beate Koksch
DOI: 10.1039/C1MB05370A

Optimality and thermodynamics determine the evolution of transcriptional regulatory networks
Marco Avila-Elchiver, Deepak Nagrath and Martin L. Yarmush
DOI: 10.1039/C1MB05177F

Interactions between CD44 protein and hyaluronan: insights from the computational study
Wojciech Plazinski and Agnieszka Knys-Dzieciuch
DOI: 10.1039/C2MB05399C

Proteome profile and biological activity of caprine, bovine and human milk fat globules
Stefano Spertino, Valentina Cipriani, Chiara De Angelis, Maria Gabriella Giuffrida, Francesco Marsano and Maria Cavaletto
DOI: 10.1039/C2MB05400K

Remember these are free to access for four weeks if you are registered with us.

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HOT: Proteomic responses of ovarian cancer cells to gold compounds

21 Dec 2011

The cytotoxicity of certain gold compounds holds promise for future cancer treatments. Treatment of ovarian cancer often involves the platinum-containing cisplatin, but drug resistance can be a problem and finding alternative therapies is required. Understanding the mechanism of drug action is an important step in developing new therapies. Proteomics can provide a picture of what effects a drug is having on a cell.

Alessandra Modesti and colleagues investigated the proteomic effects of two compounds, AuL12 and Au2Phen, on a human ovarian cancer cell line (A2780/S) using 2D-DIGE with subsequent analysis using mass spectrometry and western blotting.

Read the full story here to see what the functional analysis of the altered proteins revealed.

2D-DIGE analysis of ovarian cancer cell responses to cytotoxic gold compounds
Francesca Guidi, Michele Puglia, Chiara Gabbiani, Ida Landini, Tania Gamberi, Dolores Fregona, Maria Agostina Cinellu, Stefania Nobili, Enrico Mini, Luca Bini, Pietro Amedeo Modesti, Alessandra Modesti and Luigi Messori
Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C1MB05386H, Paper

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Molecular BioSystems now publishing Accepted Manuscripts

19 Dec 2011

Molecular BioSystems now offers you the chance to publish your accepted article as an Accepted Manuscript. This means that your research is available, in citable form, to the community even more rapidly. Find out more…

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Hot: Systematic analysis of heart transcriptome

13 Dec 2011

A key element in the study of cardiovascular disease is the use of animal models. In order for this to be useful the gene expression observed must shed light on what is happening at the same level in humans and yet how far gene expression profiles between species are conserved remains unclear.

Now Yuqi Zhao and colleagues from the Chinese Academy of Sciences Kunming Institute of Zoology in Yunnan have shed new light on this question. They analysed gene expression data from 42 normal heart samples across 5 organisms (human, rhesus, rat, mouse and dog) and evaluated the conservation of gene expression patterns of equivalent (orthologous) genes. This study may further assist the development of animal models for cardiovascular disease in the future.

Read the full story here – it’s FREE to access for 4 weeks!

A systematic analysis of heart transcriptome highlights divergent cardiovascular disease pathways between animal models and humans

Yuqi Zhao, Zizhang Sheng and Jingfei Huang
Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C1MB05415E, Paper

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Nominations for the 2012 RSC Prizes and Awards now open

05 Dec 2011

Nominations for the 2012 RSC Prizes and Awards close on the 15 January 2012

Our Prizes and Awards represent the dedication and outstanding achievements and are a platform to showcase inspiring science to gain the recognition deserved. Don’t forget to nominate colleagues who have made a significant contribution to advancing the chemical sciences.

View our full list of Prizes and Awards and use the online system to nominate a colleague.

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Themed issue on intrinsically disordered proteins just published

02 Dec 2011

We are delighted to announce the publication of our first issue for 2012, a themed issue dedicated to research on intrinsically disordered proteins, guest edited by Madan Babu, MRC, Cambridge.

The issue features a wide range of articles, from opinion pieces on cell signalling and disease mutations, to reviews on order and disorder in Gab proteins, IDPs as affinity tuners, NMR to characterise disorder, disorder in paramyxoviruses, and many hot articles.

We hope you’ll find this collection of articles informative and inspiring, for more IDP inspiration check out Madan Babu’s editorial!

View the issue

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HOT: Intrinsically disordered regions as affinity tuners in protein–DNA interactions

02 Dec 2011

In this review article Dana Vuzman and Yaakov (Koby) Levy from the Weizmann Institute of Science in Israel discuss how intrinsically disordered regions play a role in protein-DNA interactions.

Researcher insight:
Constructing a protein from two or more subdomains can enhance the jumping between different regions of the DNA. In particular, this brachiation dynamics (which is reminiscent of the way a child moves along monkey-bars) is facilitated when one of the subdomains is intrinsically disordered whose length as well as number and location of charges govern its power to promote jumping. These features of the disordered tails are fascinating also because they can be modulated in real time in the cell by post-translational modifications that may tune the affinity of the tail to the DNA.

- Koby Levy

Intrinsically disordered regions as affinity tuners in protein–DNA interactions.
Dana Vuzman and Yaakov Levy
Mol. BioSyst., 2012, 8, 47-57
DOI: 10.1039/C1MB05273J

This article is part of our themed issue on intrinsically disordered proteins and is currently free to access for 4 weeks. Don’t forget to check all the other hot articles in this issue!

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HOT: NMR to characterise intrisically disordered proteins

01 Dec 2011

In this hot review article Robert Schneider et al. looks at the problem of characterising and and understanding the conformations of intrinsically disordered proteins – no mean feat due to the the vast number of degrees of conformational freedom available to such disordered systems.

They concentrate on the use of NMR for atomic scale resolution of IDPs, developing an ensemble approach based on an algorithm nicknamed ASTEROIDS (A Selection Tool for Ensemble Representation Of Intrinsically Disordered States), to characterise the disordered state.

Researcher insight:
Intrinsically disordered proteins represent a significant, and as yet poorly understood fraction of the eurkaryotic proteome. In order to describe how these proteins work, and to provide insight into the functional advantages of such high levels of flexibility, we have developed new approaches to the description of conformational behaviour in solution, based on experimental NMR data. These methods have been applied to provide previously inaccessible ensemble models of disordered domains involved in the replication of Measles virus, human tumour repression and neurological disorders.

-Martin Blackledge

Towards a robust description of intrinsic protein disorder using nuclear magnetic resonance spectroscopy
Robert Schneider, Jie-rong Huang, Mingxi Yao, Guillaume Communie, Valéry Ozenne, Luca Mollica, Loïc Salmon, Malene Ringkjøbing Jensen and Martin Blackledge
DOI: 10.1039/C1MB05291H

This article is part of our themed issue on intrinsically disordered proteins and is currently free to access for 4 weeks. Don’t forget to check all the other hot articles in this issue!

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HOT: structural disorder in Gab proteins – implications for autoregulation and therapeutic strategies

01 Dec 2011

This hot review article Philip Simister and Stephan Feller discuss the varying levels of disorder and hidden order in large multi-site docking (LMD) proteins of the Gab family. The review includes discussions on the structural architecture of Gab proteins, how their structure is linked to disease processes and cellular networks, and finally LMD and adaptor proteins as possible therapeutic targets.

Researcher insight:
The molecular architecture of signal protein networks in cells remains very poorly understood. In this review a new concept is discussed on how seemingly disordered large docking proteins, which are thought to be essential for the molecular computation of signals from cell-surface receptors, may self-associate to adopt a more highly ordered arrangement of their disordered regions, thereby enabling better coordinated cross-talk between signalling pathways.

-Stephan Feller

Order and disorder in large multi-site docking proteins of the Gab family—implications for signalling complex formation and inhibitor design strategies
Philip C. Simister and Stephan M. Feller
DOI: 10.1039/C1MB05272A

This article is part of our themed issue on intrinsically disordered proteins and is currently free to access for 4 weeks. Don’t forget to check all the other hot articles in this issue!

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Molecular BioSystems Blog

Archive for December, 2011

Hot articles on xenobiotic screening, transcriptional regulatory networks, CD44 and more

HOT: Proteomic responses of ovarian cancer cells to gold compounds

Molecular BioSystems now publishing Accepted Manuscripts

Hot: Systematic analysis of heart transcriptome

Nominations for the 2012 RSC Prizes and Awards now open

Themed issue on intrinsically disordered proteins just published

HOT: Intrinsically disordered regions as affinity tuners in protein–DNA interactions

HOT: NMR to characterise intrisically disordered proteins

HOT: structural disorder in Gab proteins – implications for autoregulation and therapeutic strategies

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