Seasons Greetings from Molecular BioSystems!

The holidays are nearly here!!

We know everyone’s been working hard to finish off semesters and write up those papers. Here in Cambridge we’ve been working hard too, planning for the New Year and wrapping up 2013. To spread the holiday cheer, we’ve chosen three highly accessed papers and made them *FREE TO ACCESS* for the next four weeks. Enjoy!

Merry Christmas from the MBS team!



Paper: Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30, by Aaron T. Wright, Pacific Northwest National Laboratory

Paper: The structural properties of DNA regulate gene expression, by Sattar Soltani, Shahid Beheshti University

Paper: Integrated gene co-expression network analysis in the growth phase of Mycobacterium tuberculosis reveals new potential drug targets, by Srinivasan Ramachandran, Institute of Genomics and Integrative Biology, Delhi


Access is free through a registered RSC account – click here to register

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Top ten most accessed MBS articles in Q3 2013

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

Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome
Michael Bremang, Alessandro Cuomo, Anna Maria Agresta, Magdalena Stugiewicz, Valeria Spadotto and Tiziana Bonaldi
Mol. BioSyst., 2013,9, 2231-2247
DOI: 10.1039/C3LC90080K

Secretome profiling with antibody microarrays
Shakhawan Abdulrahman Mustafa, Jörg D. Hoheisel and Mohamed Saiel Saeed Alhamdani
Mol. BioSyst., 2011,7, 1795-1801
DOI: 10.1039/C3LC90080K

Network representations and methods for the analysis of chemical and biochemical pathways
Conner I. Sandefur, Maya Mincheva and Santiago Schnell
Mol. BioSyst., 2013,9, 2189-2200
DOI: 10.1039/C3MB70052F

Sirtuin 6: a review of biological effects and potential therapeutic properties
Jade M. Beauharnois, Beatriz E. Bolívar and John T. Welch
Mol. BioSyst., 2013,9, 1789-1806
DOI: 10.1039/C3MB00001J

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

Optogenetic tools for mammalian systems
Konrad Müller and Wilfried Weber
Mol. BioSyst., 2013,9, 596-608
DOI: 10.1039/C3MB25590E

Chemical biology-based approaches on fluorescent labeling of proteins in live cells
Deokho Jung, Kyoungmi Min, Juyeon Jung, Wonhee Jang and Youngeun Kwon
Mol. BioSyst., 2013,9, 862-872
DOI: 10.1039/C2MB25422K

Global signatures of protein and mRNA expression levels
Raquel de Sousa Abreu, Luiz O. Penalva, Edward M. Marcotte and Christine Vogel
Mol. BioSyst., 2009,5, 1512-1526
DOI: 10.1039/B908315D

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
Mol. BioSyst., 2013,9, 2408-2416
DOI: 10.1039/C3MB70234K

Analysis of omics data with genome-scale models of metabolism
Daniel R. Hyduke, Nathan E. Lewis and Bernhard Ø. Palsson
Mol. BioSyst., 2013,9, 167-174
DOI: 10.1039/C2MB25453K

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 MBS articles in Q2 2013

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

Cell-penetrating peptides (CPPs) as a vector for the delivery of siRNAs into cells
Ikuhiko Nakase, Gen Tanaka and Shiroh Futaki
Mol. BioSyst., 2013,9, 855-861
DOI: 10.1039/C2MB25467K

Sirtuin 6: a review of biological effects and potential therapeutic properties
Ikuhiko Nakase, Gen Tanaka and Shiroh Futaki
Mol. BioSyst., 2013,9, 855-861
DOI: 10.1039/C3MB00001J

Chemical biology-based approaches on fluorescent labeling of proteins in live cells
Deokho Jung, Kyoungmi Min, Juyeon Jung, Wonhee Jang and Youngeun Kwon
Mol. BioSyst., 2013,9, 862-872
DOI: 10.1039/C2MB25422K

Multicolor single-molecule FRET to explore protein folding and binding
Yann Gambin and Ashok A. Deniz
Mol. BioSyst., 2010,6, 1540-1547
DOI: 10.1039/C003024D

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

Multifunctional polymeric micelles with folate-mediated cancer cell targeting and pH-triggered drug releasing properties for active intracellular drug delivery
Younsoo Bae, Woo-Dong Jang, Nobuhiro Nishiyama, Shigeto Fukushima and Kazunori Kataoka
Mol. BioSyst., 2005,1, 242-250
DOI: 10.1039/B500266D

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models
Emanuel Gonçalves, Joachim Bucher, Anke Ryll, Jens Niklas, Klaus Mauch, Steffen Klamt, Miguel Rocha and Julio Saez-Rodriguez
Mol. BioSyst., 2013,9, 1576-1583
DOI: 10.1039/C3MB25489E

Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes
Young-Mo Kim, Brian J. Schmidt, Afshan S. Kidwai, Marcus B. Jones, Brooke L. Deatherage Kaiser, Heather M. Brewer, Hugh D. Mitchell, Bernhard O. Palsson, Jason E. McDermott, Fred Heffron, Richard D. Smith, Scott N. Peterson, Charles Ansong, Daniel R. Hyduke, Thomas O. Metz and Joshua N. Adkins
Mol. BioSyst., 2013,9, 1522-1534
DOI: 10.1039/C3MB25598K

Target identification of small molecules based on chemical biology approaches
Yushi Futamura, Makoto Muroi and Hiroyuki Osada
Mol. BioSyst., 2013,9, 897-914
DOI: 10.1039/C2MB25468A

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

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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Free to access HOT articles!

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

Large-scale cytological profiling for functional analysis of bioactive compounds
Marcos H. Woehrmann, Walter M. Bray, James K. Durbin, Sean C. Nisam, Alicia K. Michael, Emerson Glassey,  Joshua M. Stuart  and R. Scott Lokey  
DOI: 10.1039/C3MB70245F

Activation mechanism of claudin-4 by ephrin type-A receptor 2: a molecular dynamics approach
V. Bhavaniprasad, J. Febin Prabhu Dassa and S. Jayanthi  
DOI: 10.1039/C3MB70271E

Role of feedback and network architecture in controlling virulence gene expression in Bordetella
Mahendra Kumar Prajapata and Supreet Saini  
DOI: 10.1039/C3MB70213H

A fluorogenic probe for β-galactosidase activity imaging in living cells
Junyan Han, Myung Shin Han and Ching-Hsuan Tung  
DOI: 10.1039/C3MB70269C

The association of the cytoplasmic domains of interleukin 4 receptor alpha and interleukin 13 receptor alpha 2 regulates interleukin 4 signaling
Allison-Lynn Andrews, Ida Karin Nordgren, Gemma Campbell-Harding, John W. Holloway, Stephen T. Holgate, Donna E. Davies and Ali Tavassoli  
DOI: 10.1039/C3MB70298G

Network-based analysis of omics with multi-objective optimization
Ettore Mosca  and Luciano Milanesi  
DOI: 10.1039/C3MB70327D

Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30
Lindsey N. Anderson, David E. Culley, Beth A. Hofstad, Lacie M. Chauvigné-Hines, Erika M. Zink, Samuel O. Purvine,   Richard D. Smith, Stephen J. Callister,  Jon M. Magnuson and Aaron T. Wright 
DOI: 10.1039/C3MB70333A

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

Published on behalf of Kelly E. Theisen, web-writer for Molecular BioSystems.

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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Free to access HOT articles!

 These articles are HOT as recommended by the referees. And we’ve made them free to access for 4 weeks*

Exploring higher-order EGFR oligomerisation and phosphorylation—a combined experimental and theoretical approach
Noga Kozer, Dipak Barua, Suzanne Orchard, Eduoard C. Nice, Antony W. Burgess, William S. Hlavacek and Andrew H. A. Clayton 
DOI: 10.1039/C3MB70073A


Human cathelicidin peptide LL37 binds telomeric G-quadruplex
Jagannath Jana, Rajiv Kumar Kar, Anirban Ghosh, Atanu Biswas, Surajit Ghosh, Anirban Bhunia and Subhrangsu Chatterjee 
DOI: 10.1039/C3MB70030E


 

Urea in aqueous solution studied by quantum mechanical charge field-molecular dynamics (QMCF-MD)
Alexander K. H. Weiss and Thomas S. Hofer
DOI: 10.1039/C3MB25522K


Functional specific roles of FADD: comparative proteomic analyses from knockout cell lines
Hongqin Zhuang, Ziyi Gan, Weiwei Jiang, Xiangyu Zhang and Zi-Chun Hua
DOI: 10.1039/C3MB70023B


Extolling the benefits of molecular therapeutic lipidation
Miriam Avadisian and Patrick T. Gunning  
DOI: 10.1039/C3MB70147F


Genomics and proteomics in solving brain complexity
Beena M. Kadakkuzha and Sathyanarayanan V. Puthanveettil  
DOI: 10.1039/C3MB25391K

*Free access to individuals is provided through an RSC Publishing personal account. Registration is quick, free and simple

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Final chance to register for ISACS11 – don’t miss Shokat, Trauner, Yonath and many more!

Registration Deadline – Friday 21 June 2013

 

You have just a few days left to secure your place at the 11th conference in the International Symposia on Advancing the Chemical Sciences (ISACS) series as registration for Challenges in Chemical Biology (ISACS11) closes on Friday 21 June 2013.

Don’t miss your opportunity to join outstanding researchers from across the globe to explore the themes of immunology, microbiology, chromatin biology, epigenetics, cancer biology, systems biology and neuroscience.

Registration is quick and simple via the online booking system and spaces are filling up fast so be sure to guarantee yours now.

Programme Live

We are pleased to announce that the ISACS11 programme is now available to view online. Take a look at the schedule to discover the full speaker line up and stimulating lecture titles over the entire four days.

Find Out More

For the latest information on Challenges in Chemical Biology (ISACS11) or any of the conferences in the series, please sign up for the exclusive newsletter, follow ISACS on twitter or visit the dedicated webpage.

I look forward to welcoming you to Boston.

Best regards

Professor Ben Davis
Chairman of the Conference Committee
isacs@rsc.org

The International Symposia on Advancing the Chemical Sciences (ISACS) partner the RSC’s flagship journal Chemical Science – Winner of the ALPSP Award for Best New Journal 2011.

                    

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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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