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Introducing Molecular Omics

Molecular Omics

In 2018 Molecular BioSystems is refocusing its scope and relaunching as Molecular Omics which will focus on the –omics sciences.

Molecular Omics will publish molecular level experimental and bioinformatics research in the -omics sciences, including genomics, proteomics, transcriptomics and metabolomics. We will also welcome multidisciplinary papers presenting studies combining different types of omics, or the interface of omics and other fields such as systems biology or chemical biology.
For more information visit our website.

Now open for submissions
Molecular Omics will only accept articles which are of significant importance to their field; either fundamental research which significantly increases understanding, or research which demonstrates clear functional benefits.
In this journal we will bring the Royal Society of Chemistry’s reputation for:

  • high impact journals in areas which interface with chemistry
  • great service and times to publication
  • global reach with offices in key countries around the world

To submit, please visit: https://mc.manuscriptcentral.com/mo.

Keep in touch
If you are interested in the work that we will publish in Molecular Omics, curious about new developments in our scope, or considering the journal for your own work, then complete our form now to receive carefully selected alerts.  Sign up for e-alerts

 

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HUPO 2017 Conference

Molecular BioSystems is pleased to support the 16th Human Proteome Organization World Congress 2017.  It will be held at The Convention Centre Dublin (The CCD) from the 17th – 21st September 2017.

The conference provides a forum to present, discuss and advance proteomic research. The programme aims to consolidate existing knowledge and increase awareness of advances in the field.

This year the speakers include:

  • Leroy E. Hood: Systems Medicine, Big Data and Scientific Wellness: Transforming Healthcare—A Personal View
  • Ruedi Aebersold: The Proteome in Context
  • Ben Davis: Sugars and Proteins: Towards a Synthetic Biology
  • Albert Heck: Probing Biopharmaceutical Proteins and Protein Assemblies by Hybrid Mass Spectrometry Approaches
  • Matthias Mann: Proteomics for Signaling and Clinical Studies
  • Henry Rodriguez: Omics Convergence in Cancer Research: Advances in Precision Medicine
  • Pauline Rudd: Deciphering the Glycoproteome: a Small Step Towards Understanding the Complexity of Biological Systems
  • Matthias Uhlen: The Human Protein Atlas – Implications for Human Biology, Drug Development and Precision Medicine
  • Jenny van Eyk: Changing the Course and Impact of Chronic Disease: Personalizing Medicine
  • Atul Butte: Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease

The full programme can be found here: http://hupo2017.ie/programme/

For more information and to register please visit the website.

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Theoretical study of LIM kinase yields new inhibitors for potential cancer therapies

Hou et al. at Soochow and Zhejiang Universities in China have used various computational methods to find new inhibitors for LIM kinase 2. They have also used the same methods to evaluate the effectiveness of many existing inhibitors which have been studied experimentally, to understand why certain inhibitors might be more potent than others. Hou’s recent paper1 featured on the cover of Molecular Biosystems, Issue 10.

 

LIM kinases (LIMKs) have been found to be highly expressed in many types of tumors, and regulate several proteins crucial for cell division. Inhibitors of these kinases would therefore make possible avenues for cancer therapies. Most current inhibitors target LIMK1, one of the two isoforms that make up the LIMK family, but there is a need for improved inhibitors for LIMK2, the other isoform, and the focus of the current study.

Little research has been done on LIMK2 previously, as there is no crystal structure available in the Protein Data Bank (PDB), a requirement for theoretical models. In order to overcome this obstacle, Hour et al used homology modeling with LIMK1 to obtain a structure for LIMK2. This process used the sequence of LIMK2, and the known crystal structure of LIMK1 to produce a LIMK2 structure by established modeling programs. Due to the high level of sequence similarity (~60%), the structures for LIMK1 and LIMK2 are likely to be very similar as well. After a structure was obtained, small inhibitor molecules from an experimental study could be docked to LIMK2 and analysed computationally.

The researchers found that the flexibility of the binding site itself is extremely important for inhibitor recognition, as determined by analyzing the conformations of amino acids at the binding site before and after binding occurred. This flexibility would allow LIMK2 to bind many types and sizes of inhibitors, as observed experimentally. Additionally, the nonpolar interactions (van der Waals forces) at the binding site account for the majority of the binding energy, and can be correlated with the binding affinity of an inhibitor.

Schematic representation of interactions between a designed LIMK2 inhibitor and the modelled LIMK2

Most significantly, the researchers were able to design and test four new inhibitors based on the criteria for ideal binding affinity. These designed inhibitors have two sides connected by a linker (type II inhibitors). One side will bind to the substrate or allosteric site, while the other will bind to a nucleotide pocket, which are spatially close to each other on the surface of LIMK2. The inhibitors proposed by the researchers could later be tested experimentally, but the simulation results suggest that they will be as effective as those currently available, if not more effective.

  1. Theoretical study on the interaction of pyrrolopyrimidine derivatives as LIMK2 inhibitors:  insight into structure-based inhibitor design, Mingyun Shen, Shunye Zhou, Youyong Li, Dan Li and Tinguin Hou, Mol. BioSyst., 2013, 9, 2435-2446. DOI: 10.1039/C3MB70168A

If you would like to read more papers by Tingjun Hou et al, please click here!

Or for more MBS HOT papers, browse the blog.

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Free to access HOT articles!

These HOT articles have been recommended by our referees and are free to access for 4 weeks*

An in silico exploration of the interaction mechanism of pyrazolo[1,5-a]pyrimidine type CDK2 inhibitors
Yan Li, Weimin Gao, Feng Li, Jinghui Wang, Jingxiao Zhang, Yinfeng Yang, Shuwei Zhang and Ling Yang  
DOI: 10.1039/C3MB70186G 

GA 

Theoretical study on the interaction of pyrrolopyrimidine derivatives as LIMK2 inhibitors: insight into structure-based inhibitor design
Mingyun Shen, Shunye Zhou, Youyong Li, Dan Li and Tingjun Hou
DOI: 10.1039/C3MB70168A

GA

Selective inhibition of the unfolded protein response: targeting catalytic sites for Schiff base modification
Susana M. Tomasio, Heather P. Harding, David Ron, Benedict C. S. Cross and Peter J. Bond 
DOI: 10.1039/C3MB70234K

GA

The three-dimensional context of a double helix determines the fluorescence of the internucleoside-tethered pair of fluorophores
Valeri Metelev, Surong Zhang, David Tabatadze, Anand T. N. Kumar and Alexei Bogdanov
DOI: 10.1039/C3MB70108E

GA 

BH3 helix-derived biophotonic nanoswitches regulate cytochrome c release in permeabilised cells
Robert J. Mart, Rachel J. Errington, Catherine L. Watkins, Sally C. Chappell, Marie Wiltshire, Arwyn T. Jones, Paul J. Smith and Rudolf K. Allemann  
DOI: 10.1039/C3MB70246D

GA

Metabolomic identification of diagnostic plasma biomarkers in humans with chronic heart failure

Juan Wang, Zhongfeng Li, Jianxin Chen, Huihui Zhao, Liangtao Luo, Chan Chen, Xuegong Xu, Wenting Zhang, Kuo Gao, Bin Li, Junpeng Zhang and Wei Wang
DOI: 10.1039/C3MB70227H

GA

*Free access to individuals is provided through an RSC Publishing personal account. It’s quick, simple and more importantly – free – to register!

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Molecular Biosystems: The Most Cited Articles of 2010 and 2011

The editors here at MBS want to highlight the Journal’s most cited articles of 2010 and 2011, and to take the opportunity to showcase some of the fantastic work that our authors have produced over the last two years. Congratulations to everyone!

As of now, all of the below articles will be free for 4 weeks (until Monday 16th Sept),* so make the most of this opportunity to download the full papers!

Top 3 Cited Reviews:

  1. LF Peng et. al.: Small-molecule modulators of the Sonic Hedgehog signaling pathway (DOI: 10.1039/b910196a).

    A review on our current understanding of small-molecule modulators of Sonic hedgehog (Shh) signalling, and at which points in the pathway modulators are active. Peng and colleagues go on to include discussion of modulator application in therapeutics and our current understanding of this phenomenon.


  2. V Torchilin et. al.: Intracellular transduction using cell-penetrating peptides  (DOI: 10.1039/b916297f).

    A review highlighting the mechanisms of cell penetrating peptide (CPP)-mediated deliver of various agents, including peptides, proteins and small molecules. Torchilin and colleagues go on to provide excellent examples to illustrate the potential use of CPPs in biology and medicine.


  3. SJ Baserja: When ribosomes go bad: diseases of ribosome biogenesis (DOI: 10.1039/b919670f).

    A review highlighting diseases of ribosome biogenesis, a biological error which was, until recently, assumes to be lethal. Baserga and colleagues discuss our limitations in understanding the molecular mechanisms underlying these diseases.


Top 10 Cited Research Papers:

  1. XA Xiao et. al.: GPCR-2L: predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions (DOI: 10.1039/c0mb00170h).

    Xiao and colleagues develop a new predictor for G-protein coupled receptors (GPCRs) by hybridising two different modes of pseudo-amino acid composition. Their predictor displays high success rates and has potential application in drug development.


  2. XA Xiao et. al.: iLoc-Plant: a multi-label classifier for predicting the subcellular localization of plant proteins with both single and multiple sites (DOI: 10.1039/c1mb05232b).

    Xiao and colleagues develop a new predictor for the sub-cellular localisation of plant proteins, which introduces ‘multi-labeled learning’, allowing for the detection of multiple-location proteins.


  3. SC Connor et. al.: Integration of metabolomics and transcriptomics data to aid biomarker discovery in type 2 diabetes (DOI: 10.1039/b914182k).

    A paper on non-targeted metabolomics technologies and their use in providing novel biomarkers of disease and drug efficacy. Combined analysis of analysis of metabolite and gene expression changes revealed 24 distinct pathways that were altered in the diabetic model.


  4. A Salvati et. al.: Time and space resolved uptake study of silica nanoparticles by human cells (DOI: 10.1039/c0mb00109k)

  5. JS Hartig et. al.: A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression (DOI: 10.1039/b923076a)

  6. CJ Schofield et. al.: A miniaturized screen for inhibitors of Jumonji histone demethylases (DOI: 10.1039/b912993f)

  7. BF Cravatt et. al.: Characterization of mice lacking candidate N-acyl ethanolamine biosynthetic enzymes provides evidence for multiple pathways that contribute to endocannabinoid production in vivo (DOI: 10.1039/c000237b)

  8. TDH Bugg et. al.: Development of novel assays for lignin degradation: comparative analysis of bacterial and fungal lignin degraders (DOI: 10.1039/b908966g)

  9. JB Bramsden et. al.: Utilization of unlocked nucleic acid (UNA) to enhance siRNA performance in vitro and in vivo (DOI: 10.1039/b918869j)

  10. SS Sidhu et. al.: Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing (DOI: 10.1039/c0mb00061b)

   

*free through an RSC account

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Take 1.. minute for chemistry in health

Do you know how chemical scientists can tackle global challenges in Human Health? If so, the RSC is running a one minute video competition this summer for young researchers such as PhD and Post-doc students; get involved and innovate the way scientists share their research. Your video should communicate your own personal research or an area of research that interests you, highlighting its significance and impact to Human Health.

Five videos will be shortlisted by our judging panel and the winner will be selected during the ‘How does chemistry keep us healthy?’ themed National Chemistry Week taking place 16-23 November. 

A £500 prize and a fantastic opportunity to shadow the award winning video Journalist, Brady Harran, is up for grabs for the winner.

The judging panel will include the makers of The Periodic Tale of Videos, Martyn Poliakoff and Brady Harran, and RSC Division representatives.

Check out our webpage for further details of the competition and an example video. 

The competition will open 02 April 2013 and the closing date for entries is 01 July 2013. Please submit your entries to rsc.li/take-1-video-competition.

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Themed Issue 4 online now! Reviews from the Editorial and Advisory Board members

The fun outside front cover features the contribution of Seung Bum Park, MBS Associate Editor based at Seoul National University, Korea, to this month’s special issue featuring work from many of our Editorial and Advisory Board members. Seung Bum Park and colleagues review methods for identifying the targets of bioactive small molecules, the difficulties faces and the new shift towards covalent bonds via use of chemoreactive groups changing the nature of target protein identification.

From noncovalent to covalent bonds: a paradigm shift in target protein identification
Jongmin Park, Minseob Koh and Seung Bum Park
DOI: 10.1039/C2MB25502B

Editorial Board member Ulrike Eggert and colleague Xin Zhang review the more unusual, overlooked functions of G protein-coupled receptors in cells, such as in membrane trafficking and cell division in addition to their more widely known roles in cell signalling.

Non-traditional roles of G protein-coupled receptors in basic cell biology
Xin Zhang and Ulrike S. Eggert
DOI: 10.1039/C2MB25429H

Wilfred Weber, also a member of the Editorial Board, and Jonrad Muller at University of Freiburg, Germany, provide a fascinating look at how we can control biological processes in mammalian cells by the manipulation of light using optogenetic tools in their review article:

Optogenetic tools for mammalian systems
Konrad Müller and Wilfried Weber
DOI: 10.1039/C3MB25590E

 

These are just a couple of examples of the high quality review articles produced by board members past and present for this themed issue. Have a look at the whole issue here to see the ones that are of interest to you.

This issue also still contains plenty of high quality primary research articles in chemical biology, -omics and systems biology, including several HOT communications and articles such as:

Identifying subcellular localizations of mammalian protein complexes based on graph theory with a random forest algorithm
Zhan-Chao Li, Yan-Hua Lai, Li-Li Chen, Chao Chen, Yun Xie, Zong Dai and Xiao-Yong Zou
DOI: 10.1039/C3MB25451H

Protein intrinsic disorder in the acetylome of intracellular and extracellular Toxoplasma gondii
Bin Xue, Victoria Jeffers, William J. Sullivan and Vladimir N. Uversky
DOI: 10.1039/C3MB25517D

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A review – it takes two to tango if you’re a Raf kinase

Researchers at University College Dublin, Anglela Baljuls, Boris Kholodenko and Walter Kolch, look at the role of dimerization of Raf kinases in the MEK-ERK pathway in cancer and the implications for design of drug therapies in this recent review.

Raf tango signallingThe MEK-ERK pathway is involved in the effect that extracellular stimuli have on processes happening inside the cell, such as proliferation and apoptosis to name just two. Mutations of the proteins in this pathway can result in them being stuck in the inactive or active form, giving rise in many cases to different forms of cancer. Raf is a group of proteins central to this signalling pathway. The regulation of active and inactive forms of Raf is complicated, but Raf dimerization is known to play a part. This in-depth review examines:

1. Inducing and inhibiting Raf dimerisation

2. Why dimerization is necessary

3. How does dimerization affect cell proliferation and tumour formation?

4. Targeting Raf and drug inhibitor design

As pointed out in the review, Raf has made the headlines as an important piece of the puzzle with regard to cancer treatment, but this review shows that research on Raf regulation is ongoing with dimerization playing a critical role.

Read the full review here:

It takes two to tango – signalling by dimeric Raf kinases
Angela Baljuls, Boris N. Kholodenko and Walter Kolch
DOI: 10.1039/C2MB25393C

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Top ten most accessed articles in August 2012

The following articles in Molecular BioSystems were in the top ten most accessed for August:

Metabolome 2.0: quantitative genetics and network biology of metabolic phenotypes
Marc-Emmanuel Dumas
Mol. BioSyst., 2012, 8, 2494-2502
DOI: 10.1039/C2MB25167A

Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions
Kristen M. Naegle, Forest M. White, Douglas A. Lauffenburger and Michael B. Yaffe
Mol. BioSyst., 2012, 8, 2771-2782
DOI: 10.1039/C2MB25200G

Optimized TAL effector nucleases (TALENs) for use in treatment of sickle cell disease
Ning Sun, Jing Liang, Zhanar Abil and Huimin Zhao
Mol. BioSyst., 2012, 8, 1255-1263
DOI: 10.1039/C2MB05461B 

Upregulated MALAT-1 contributes to bladder cancer cell migration by inducing epithelial-to-mesenchymal transition
Liang Ying, Qi Chen, Yawei Wang, Zhihua Zhou, Yiran Huang and Feng Qiu
Mol. BioSyst., 2012, 8, 2289-2294
DOI: 10.1039/C2MB25070E

Synthetic lethal interactions in yeast reveal functional roles of J protein co-chaperones
Anne T. Gillies, Rebecca Taylor and Jason E. Gestwicki
Mol. BioSyst., 2012, 8, 2901-2908
DOI: 10.1039/C2MB25248A

Emerging investigators contributors 2012
Mol. BioSyst., 2012, 8, 2461-2465
DOI: 10.1039/C2MB90034C

Inhibitors targeting on cell wall biosynthesis pathway of MRSA
Haihong Hao, Guyue Cheng, Menghong Dai, Qinghua Wu and Zonghui Yuan
Mol. BioSyst., 2012, 8, 2828-2838
DOI: 10.1039/C2MB25188D

The changes of microRNA expression profiles and tyrosinase related proteins in MITF knocked down melanocytes
Ping Wang, Yong Li, Weisong Hong, Junhui Zhen, Jingping Ren, Zhao Li and Aie Xu
Mol. BioSyst., 2012, 8, 2924-2931
DOI: 10.1039/C2MB25228G

LC-MS-based metabolomics
Bin Zhou, Jun Feng Xiao, Leepika Tuli and Habtom W. Ressom
Mol. BioSyst., 2012, 8, 470-481
DOI: 10.1039/C1MB05350G

Large-scale quantitative glycoproteomics analysis of site-specific glycosylation occupancy
Sheng Pan, Yasuko Tamura, Ru Chen, Damon May, Martin W. McIntosh and Teresa A. Brentnall
Mol. BioSyst., 2012, 8, 2850-2856
DOI: 10.1039/C2MB25268F

Why not take a look at the articles today and blog your thoughts and comments below.

Fancy submitting an article to Molecular BioSystems? Then why not submit to us today or alternatively email us your suggestions.

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Top ten most accessed articles in July 2012

This month sees the following articles in Molecular BioSystems that are in the top ten most accessed:

Optimized TAL effector nucleases (TALENs) for use in treatment of sickle cell disease  
Ning Sun, Jing Liang, Zhanar Abil and Huimin Zhao  
Mol. BioSyst., 2012, 8, 1255-1263
DOI: 10.1039/C2MB05461B  

Intramolecular three-colour single pair FRET of intrinsically disordered proteins with increased dynamic range  
Sigrid Milles, Christine Koehler, Yann Gambin, Ashok A. Deniz and Edward A. Lemke  
Mol. BioSyst., 2012, 8, 2531-2534
DOI: 10.1039/C2MB25135C  

Rewiring the dynamic interactome 
Melissa J. Davis, Chang Jin Shin, Ning Jing and Mark A. Ragan  
Mol. BioSyst., 2012, 8, 2054-2066
DOI: 10.1039/C2MB25050K  

Identification of DNA–protein complexes using an improved, combined western blotting-electrophoretic mobility shift assay (WEMSA) with a fluorescence imaging system  
Klaus Deckmann, Florian Rörsch, Gerd Geisslinger and Sabine Grösch  
Mol. BioSyst., 2012, 8, 1389-1395
DOI: 10.1039/C2MB05500G  

Upregulated MALAT-1 contributes to bladder cancer cell migration by inducing epithelial-to-mesenchymal transition  
Liang Ying, Qi Chen, Yawei Wang, Zhihua Zhou, Yiran Huang and Feng Qiu  
Mol. BioSyst., 2012, 8, 2289-2294
DOI: 10.1039/C2MB25070E  

Interaction and photo-induced cleavage studies of a copper based chemotherapeutic drug with human serum albumin: spectroscopic and molecular docking study    
Sartaj Tabassum, Waddhaah M. Al-Asbahy, Mohd. Afzal, Farukh Arjmand and Rizwan Hasan Khan  
Mol. BioSyst., 2012, 8, 2424-2433
DOI: 10.1039/C2MB25119A

Split-superpositive GFP reassembly is a fast, efficient, and robust method for detecting protein–protein interactions in vivo  
Brett D. Blakeley, Alex M. Chapman and Brian R. McNaughton  
Mol. BioSyst., 2012, 8, 2036-2040
DOI: 10.1039/C2MB25130B  

Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering  
Pau Bernadó and Dmitri I. Svergun  
Mol. BioSyst., 2012, 8, 151-167
DOI: 10.1039/C1MB05275F  

Differential RNAi screening provides insights into the rewiring of signalling networks during oxidative stress  
Mar Arias Garcia, Miguel Sanchez Alvarez, Heba Sailem, Vicky Bousgouni, Julia Sero and Chris Bakal 
Mol. BioSyst., 2012, 8, 2605-2613
DOI: 10.1039/C2MB25092F  

Small-molecule modulators of the Sonic Hedgehog signaling pathway 
Benjamin Z. Stanton and Lee F. Peng  
Mol. BioSyst., 2010, 6, 44-54
DOI: 10.1039/B910196A  

Why not take a look at the articles today and blog your thoughts and comments below.

Fancy submitting an article to Molecular BioSystems? Then why not submit to us today or alternatively email us your suggestions.

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