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Proteomics 2013 themed issue online now!

07 May 2013

The Proteomics 2013 issue is introduced by the President of the Italian Proteomics Association Andrea Urbani et al. following on from the ItPA meeting in June 2012.

This is followed by an Opinion piece from Matthias Gstaiger and Ruedi Aebersold at ETH Zurich, Switzerland, on the increasing understanding of genotype-phenotype relationships due to deciphering proteome organisation.

Digital and analogical reality in proteomics investigation
Andrea Urbani, Massimo Castagnola, Mauro Fasano, Luca Bini, Alessandra Modesti, Anna Maria Timperio and Paola Roncada
DOI: 10.1039/C3MB90013D

Genotype–phenotype relationships in light of a modular protein interaction landscape
Matthias Gstaiger and Ruedi Aebersold
DOI: 10.1039/C3MB25583B

Amongst the three review articles in this Proteomics themed issue, a HOT review article by Jorg Stulke et al. at Georg-August-Universitat Gottingen, Germany, is featured on the front cover. This review taking a fresh look at the genes and proteins of Bacillus subtilis was featured on the blog recently. It highlights the difficulties with defining the essential genes of a particular organism.

Essential genes in Bacillus subtilis: a re-evaluation after ten years
Fabian M. Commichau, Nico Pietack and Jörg Stülke
DOI: 10.1039/C3MB25595F

The inside front cover features work from Damiana Pieragostino et al. in Italy in which shotgun proteomics is used to provide a profile of the proteins in the tears of patients with primary open angle glaucoma. They find a mix of inflammatory proteins as possible biomarkers for early diagnosis of the disease, which is a major global cause of blindness.

Shotgun proteomics reveals specific modulated protein patterns in tears of patients with primary open angle glaucoma naïve to therapy
Damiana Pieragostino, Luca Agnifili, Vincenzo Fasanella, Simona D’Aguanno, Rodolfo Mastropasqua, Carmine Di Ilio, Paolo Sacchetta, Andrea Urbani and Piero Del Boccio
DOI: 10.1039/C3MB25463A

The Proteomics issue is packed with more reviews, communications, a Method article and several HOT articles, see the full contents list here.

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Emerging Investigators 2012

11 Sep 2012

We are delighted to publish our third themed issue dedicated to the work of new and emerging investigators whose research in chemical biology interfaces with the -omic sciences and systems biology.

There is plenty of exciting research in this issue, including work from Priscilla Yang on exploiting known kinase inhibitors to develop new probes for imaging kinases and Nuno Bandeira on spectral networks algorithms to analyse tandem mass spectroscopy results. Both these articles are free to access for the next four weeks.

For all the contributors to the issue please see our Profile article.

To coincide with this, Molecular BioSystems Deputy Editor Victoria Eyley has just returned from the International Conference on Systems Biology (ICSB) in Toronto, Canada where she presented this year’s Early Career Lectureship to Thijn Brummelkamp (The Netherlands Cancer Institute). Thijn is being recognised as he was one of the first to describe stable RNA interference, which is widely used to study gene function.

*Free access is provided to subscribing institutions or through an RSC Publishing Personal Account. Registration is quick and easy at http://pubs.rsc.org/en/account/register.

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Italian Proteomics themed issue just published

13 Mar 2012

Issue 4 of Molecular BioSystems focuses on proteomics, including a collection of articles from the latest Italian Proteomics Association’s National Congress held in Turin last year. On the cover the editorial introduction to the issue by the Directory Board of the Italian Proteomics Association:

Integrative proteomics: perspective in complex system interpretation
Andrea Urbani, Alessandra Modesti, Anna Maria Timperio, Luca Bini, Massimo Castagnola, Mauro Fasano and Paola Roncada
DOI: 10.1039/C2MB90009B

Issue 4 inside front cover On the inside front cover is a HOT article by Swadha Anand and Debasisa Mohanty at the National Institute of Immunology, India, where they investigate the role of inter-domain movements in substrate channeling by carrying out a series of explicit solvent molecular dynamics simulations.

Inter-domain movements in polyketide synthases: a molecular dynamics study
Swadha Anand and Debasisa Mohanty
DOI: 10.1039/C2MB05425F

Below is a selection of the proteomics-themed papers included in this issue:

Modulation of urinary peptidome in humans exposed to high altitude hypoxia
Veronica Mainini et al.
DOI: 10.1039/C1MB05377A

GENOCOP algorithm and hierarchical grid transformation for image warping of two dimensional gel eletrophoretic maps
Emilio Marengo et al.
DOI: 10.1039/C2MB05396A

Differential protein expression in tears of patients with primary open angle and pseudoexfoliative glaucoma
Damiana Pieragostino et al.
DOI: 10.1039/C1MB05357D

Proteomic analysis in clear cell renal cell carcinoma: identification of differentially expressed protein by 2-D DIGE
Marina Pitto et al.
DOI: 10.1039/C2MB05390J

Comparative proteomics to evaluate multi drug resistance in Escherichia coli
Paola Roncada et al.
DOI: 10.1039/C1MB05385J

Read the rest of Issue 4 here

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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: 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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HOT: Intrinsically disordered GTPase from Bacillus pasteurii

29 Nov 2011

In this paper Barbara Zambelli and colleagues discuss the first known intrinsically disordered enzyme which exhibits activity in its disordered state. This protein, BpUreG, from Bacillus pasteurii exists in three different forms depending on the temperature and concentration of denaturant used.

Researcher insight:
Intrinsic disorder is well known to play a role in some key regulative functions in proteins, while enzymatic activity is generally associated with overall protein rigidity, and only few cases of artificial intrinsically disordered enzymes have been reported so far. The present study provides insights into the folding landscape sampled by BpUreG, the first discovered native intrinsically disordered enzyme, known to be active in its unstructured state. A combination of spectroscopic and calorimetric techniques revealed that this enzyme exists as an ensemble of uncooperatively interconverting conformational states, whose degree of structure depends on temperature and denaturant concentration.

- Barbara Zambelli

Insights in the (un)structural organization of Bacillus pasteurii UreG, an intrinsically disordered GTPase enzyme
Barbara Zambelli, Nunilo Cremades, Paolo Neyroz, Paola Turano, Vladimir N. Uversky and Stefano Ciurli
Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C1MB05227F, Paper

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: Intrinsic disorder in the androgen receptor – identification, characterization and drugability

28 Nov 2011

This review article by Iain J McEwan focusses on the androgen receptor (AR) which regulates gene expression in response to testosterone and dihydrotestosterone. The ‘collapsed disordered’ structure of the N-terminal portion of the molecule is discussed in relation to its role in protein-protein interactions and as a potential target site for drug action.

Researcher insight:
The structurally plastic N-terminal domain (NTD) of steroid receptors is important for both receptor function and allosteric regulation; and adopts a helical conformation upon receptor binding to DNA and co-regulatory proteins. In an exciting recent development the function of this region of the androgen receptor was found to be directly inhibited by a small molecule, which switched off receptor activity in a wide range of functional assays.

- Iain J. McEwan

Intrinsic disorder in the androgen receptor: identification, characterisation and drugability
Iain J. McEwan
Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C1MB05249G, Review

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: new insights into alpha-synuclein permeabilisation mechanisms in Parkinson’s disease

25 Nov 2011

This hot article from Martin Stöckl et al. provides new insight into the toxic role of α-synuclein – a protein associated with the development and progression of Parkinson’s disease.

α-synuclein oligomers are thought to cause neuronal death by permeabilising the cellular membrane. Here Stöckl et al. show that more than one mechanism may be active to cause this – oligomers could form pores allowing the passage of small molecules into the neurons by insertion into membranes or their interaction with the membrane may disrupt lipid packing, resulting in membrane defects. They also show that α-synuclein increases the flip-flop rate of the lipid membranes.

Researcher insight:
Oligomeric forms of α-synuclein are thought to impair cellular membrane integrity in the development of Parkinson’s Disease (PD). This study demonstrates that oligomeric α-synuclein not only permeabilizes lipid bilayers, but also causes an enhanced lipid flip-flop between the outer and inner leaflets, revealing a novel mechanism which could contribute to membrane destabilization and eventually neuronal death in PD.

-Vinod Subramaniam

Kinetic measurements give new insights into lipid membrane permeabilization by α-synuclein oligomers
Martin Stöckl, Mireille M. A. E. Claessens and Vinod Subramaniam
DOI: 10.1039/C1MB05293D

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: exploring mechanisms of long distance cell signal travel

23 Nov 2011

Ruth Nussinov, NCI-Frederick, discusses the possible mechanisms that support long-range signalling in cells in this hot Opinion article.

She proposes that three key properties have evolved to enable signals to travel rapidly over comparatively vast cellular distances: 1) modular organisation according to protein function, 2) sequences are ‘pre-encoded’ to facilitate signalling and 3) intrinsically disordered proteins enable fast signal transmission through dense packing.

Researcher insight:

This paper proposes that conformational disorder can help faster propagation of signals across the cell. When disordered proteins bind, their interface is tightly packed. Dense packing facilitates efficient transmission of the allosteric energy wave, which leads to fast cellular response to external stimuli.

-Ruth Nussinov

How do dynamic cellular signals travel long distances?
Ruth Nussinov
DOI: 10.1039/C1MB05205E

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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Blogs Home

Molecular BioSystems Blog

Archive for the ‘Themed Issues’ Category

Proteomics 2013 themed issue online now!

Emerging Investigators 2012

Italian Proteomics themed issue just published

Themed issue on intrinsically disordered proteins just published

HOT: NMR to characterise intrisically disordered proteins

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

HOT: Intrinsically disordered GTPase from Bacillus pasteurii

HOT: Intrinsic disorder in the androgen receptor – identification, characterization and drugability

HOT: new insights into alpha-synuclein permeabilisation mechanisms in Parkinson’s disease

HOT: exploring mechanisms of long distance cell signal travel

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