Protein labelling themed issue announced

We are pleased to announce an upcoming Molecular BioSystems issue on protein labelling. The Guest Editors for this issue are Dr Lyn Jones (Pfizer, USA) and Professor Eranthie Weerapana (Boston College, USA).

Scope

This issue will cover the discovery, development and application of protein labelling to advance chemical biology. Relevant topics include:

  • Bioconjugation and site-specific labelling
  • Activity-based protein profiling
  • Target identification and validation
  • New click reactions
  • Chemical mutagenesis
  • Advances in –omics technologies underpinned by breakthroughs in protein labelling techniques
  • Imaging and screening technologies
  • Advances in pharmacological and therapeutic modalities (e.g. hydrophobic tagging, synthetic vaccines, antibody-drug conjugates)

Deadline for Submission: 11 December 2015

Please e-mail the Editorial Office if you are interested in contributing an article.

Manuscripts can be submitted using the Royal Society of Chemistry’s online article submission service. Please clearly state that the manuscript is submitted for the themed issue on protein labelling. The level of quality of this issue will be high, and all manuscripts will undergo the journal’s normal peer review processes.

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10th annual meeting of Japanese Society for Chemical Biology

The 10th annual meeting of the Japanese Society for Chemical Biology was held in Sendai from 10-12th June 2015 and Molecular BioSystems was pleased to award two poster prizes.

Congratulations to the winners:

Mizuki Watanabe (left) , an Assistant Professor for Professor Uesugi Motonari at Kyoto University, for his poster entitled:
The action mechanism of endogenous small molecules that suppress the lipid biosynthesis

Syusuke Egoshi (right), working for Professor Minoru Ueda at Tohoku University, for his poster entitled:
In vivo Raman Imaging in living guard cells for elucidating the localization of the plant toxin coronatine

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Drawing order from disorder to unravel Ebola’s lethality

Christopher Barnard writes about a hot Molecular BioSystems article for Chemistry World

The virulence of Ebola virus strains appears to be innately linked to the degree of disorder in proteins that form their nucleocapsids. Computational analysis has revealed that strains responsible for the most lethal outbreaks of Ebola show significantly higher levels of intrinsic protein disorder than less virulent strains, in a discovery that could constitute a major breakthrough in understanding the pathogen’s behaviour.

With over 27,000 confirmed, probable and suspected cases and more than 11,000 fatalities worldwide, the ongoing Ebola outbreak has resulted in considerably more casualties since late 2013 than all other outbreaks combined. There are no effective treatments or vaccines against the haemorrhagic fever that evinces Ebola infection; however, strains of the virus with drastically different virulence have emerged since the first outbreak in 1976, with fatality rates ranging from 25 to 90%.

In an effort to explain such radical variations in lethality, researchers Gerard Goh, from Goh’s BioComputing in Singapore, Keith Dunker, from the Indiana University School of Medicine in the US, and Vladimir Uversky, from the University of South Florida in the US, have computationally explored links between the virulence of different Ebola virus strains and their predicted protein structures. The group discovered that intrinsically disordered proteins (IDPs) encapsidating the virus’ genetic material appear to play a large role, with increasing levels of disorder correlating with greater virulence.


Read the full story in Chemistry World»

Read the original journal article in Molecular BioSystems – it is free to access until 24 July 2015.

Detection of links between Ebola nucleocapsid and virulence using disorder analysis
Gerard Kian-Meng Goh, Keith Dunker and Vladimir N. Uversky
Mol. BioSyst., 2015, Accepted Manuscript
DOI: 10.1039/C5MB00240K, Paper

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Editor’s Choice: Chemical Biology

Looking for the best articles in Chemical Biology?

Dr Lyn Jones, Editorial Board member

Molecular BioSystems Editorial Board member Dr Lyn Jones (Pfizer) has picked some of his favourite articles recently published in the journal. You can read these articles for free for a limited period by clicking on the links below.

Did you know?

Molecular BioSystems publishes experimental and theoretical research at the interface of chemistry and biology, covering both chemical tools for biological questions, and molecular-level understanding, control and manipulation of biological processes. Access our full scope

As a journal published by the Royal Society of Chemistry, Molecular BioSystems benefits from free colour artwork, no page charges, attractive journal design and a professional editorial team. The journal is included in MEDLINE, ISI and SCOPUS and is NIH compliant.

Read our chemical biology Editor’s Choice selection for FREE today:

Probing the effect of an inhibitor of an ATPase domain of Hsc70 on clathrin-mediated endocytosis
Hyungseoph J. Cho, Gun-Hee Kim, Seong-Hyun Park, Ji Young Hyun, Nak-Kyoon Kim and Injae Shin
Mol. BioSyst., 2015, Advance Article
DOI:
10.1039/C4MB00695J

Selection of LNA-containing DNA aptamers against recombinant human CD73
Ida C. Elle, Kasper K. Karlsen, Mikkel G. Terp, Niels Larsen, Ronni Nielsen, Nicola Derbyshire, Susanne Mandrup, Henrik J. Ditzel and Jesper Wengel
Mol. BioSyst., 2015,11, 1260-1270
DOI: 10.1039/C5MB00045A

Probing the effect of minor groove interactions on the catalytic efficiency of DNAzymes 8–17 and 10–23
Michael H. Räz and Marcel Hollenstein
Mol. BioSyst., 2015,11, 1454-1461
DOI: 10.1039/C5MB00102A

You can find many more excellent articles on chemical biology on our dedicated online collection at :

http://rsc.li/mb-chemical-biology

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Meet the MBS team – See where and when you can meet us in 2015

A selection of conferences the journal will be attending in 2015.

The Molecular BioSystems team will be attending a number of conferences in 2015 and we would be delighted to meet you there.

We’re also the team behind Molecular BioSystems’ sister journals OBC, MedChemComm, and Natural Product Reviews, so we’ll happily discuss your interdisciplinary research work. In fact, many of our authors choose to publish their research across all of these titles.

Spring

National symposium on Chemical Biology 18-19 February 2015, Mysore, India. Meet Deeksha Gupta.

Directing Biosynthesis IV 25 – 27th March 2015, Norwich, UK. Meet Marie Cote.

MedChemComm, 27-30 April 2015, Hyderabad, India. Meet Deeksha Gupta.

Grassmere Heterocyclic meeting 7th – 11th May, 2015, Grassmere, UK. Meet James Anson.

Summer

Royal Society of Chemistry Organic Chemistry Symposium Series 1st – 5th June 2015, Sendai, Tokyo, Kyoto, Japan. Meet Rich Kelly

American Peptide Symposium 20th – 25th June 2015, Orlando, Florida. Meet Rich Kelly.

ISMSC 28th June – 2nd July 2015, Strasbourg, France. Meet Marie Cote.

7th International Conference on Green and Sustainable Chemistry, July 5 – 8th, Tokyo, Japan. Meet Hiromitsu Urakami.

ESOC 2015 12th – 16th July 2015, Lisbon, Portugal. Meet Marie Cote.

RSC Organic Synthesis 20th – 23rd July 2015, Cambridge, UK. Meet James Anson.

9th CCS National Organic Chemistry conference, 31st July to 3rd August 2015, Changchun, China. Meet Guanqun Song.

9th National Chemical Biology conference, August, Tianjin, China. Meet Guanqun Song.

250th ACS National Meeting & Exposition 16th – 20th August 2015, Boston, USA.

25th International Society of Heterocyclic Chemistry Conference (August 23-28) in Santa Barbara, USA. Meet Jennifer Lee.

Autumn

18th RSC/SCI medicinal chemistry conference 13th – 16th September 2015, Cambridge, UK. Meet James Anson.

26th Symposium on Physical Organic Chemistry, 24 – 26th September, Ehime, Japan. Meet Hiromitsu Urakami.

13th International Kyoto Conference on New Aspects of Organic Chemistry , 9th – 13th November, Kyoto, Japan. Meet Hiromitsu Urakami.

Tateshina Conference, 13th – 15th November, Tateshina, Japan. Meet Hiromitsu Urakami.

BMOS-16 15th – 19th November 2015, Buzios, Brazil. Meet Rich Kelly.

Winter

Pacifichem 15th – 20th December 2015, Hawaii, USA. Meet Marie Cote.

Let us know if you are planning on attending any of these meetings, as we would be happy to meet you there!

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Recent HOT Molecular BioSystems articles

The following HOT articles have been highlighted by the reviewers of the articles as being particularly interesting or significant pieces of research. These are all free to access until 28th February 2015. The order they appear in the list has no meaning or ranking.


Applications of mass spectrometry for cellular lipid analysis
Chunyan Wang, Miao Wang and Xianlin Han  
DOI: 10.1039/C4MB00586D, Review Article

C4MB00586D GA


Systems biology approach to understanding post-traumatic stress disorder
Gunjan S. Thakur, Bernie J. Daigle Jr, Kelsey R. Dean, Yuanyang Zhang, Maria Rodriguez-Fernandez, Rasha Hammamieh, Ruoting Yang, Marti Jett, Joseph Palma, Linda R. Petzold and Francis J. Doyle III  
DOI: 10.1039/C4MB00404C, Review Article

C4MB00404C GA


An integrated analysis of differential miRNA and mRNA expressions in human gallstones
Bin Yang, Bin Liu, Pinduan Bi, Tao Wu, Qiang Wang and Jie Zhang  
DOI: 10.1039/C4MB00741G, Paper

C4MB00741G GA


Hierarchical control of coherent gene clusters defines the molecular mechanisms of glioblastoma
Igor F. Tsigelny, Valentina L. Kouznetsova, Pengfei Jiang, Sandeep C. Pingle and Santosh Kesari  
DOI: 10.1039/C5MB00007F, Paper

C5MB00007F GA


Cancer-associated fibroblasts induce trastuzumab resistance in HER2 positive breast cancer cells
Yan Mao, Yuzi Zhang, Qing Qu, Meizhong Zhao, Ying Lou, Junjun Liu, Ou huang, Xiaosong Chen, Jiayi Wu and Kunwei Shen  
DOI: 10.1039/C4MB00710G, Paper

C4MB00710G GA


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Recent HOT Molecular BioSystems articles

The following HOT articles have been highlighted by the reviewers of the articles as being particularly interesting or significant pieces of research. These are all free to access until 31st January 2015. The order they appear in the list has no meaning or ranking.

Cysteine-mediated redox signalling in the mitochondria
D. W. Bak and E. Weerapana  
DOI: 10.1039/C4MB00571F, Review Article

C4MB00571F GA


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What are your colleagues reading in Molecular BioSystems?

The articles below are the most read Molecular BioSystems articles in July, August and September 2014.

Isothermal amplified detection of DNA and RNA
Lei Yan, Jie Zhou, Yue Zheng, Adam S. Gamson, Benjamin T. Roembke, Shizuka Nakayama and Herman O. Sintim 
DOI: 10.1039/C3MB70304E

Logical modelling of Drosophila signalling pathways
Abibatou Mbodj, Guillaume Junion, Christine Brun, Eileen E. M. Furlong and Denis Thieffry
DOI: 10.1039/C3MB70187E

Concerted bioinformatic analysis of the genome-scale blood transcription factor compendium reveals new control mechanisms
Anagha Joshi and Berthold Gottgens  
DOI: 10.1039/C4MB00354C

A metabolomics approach for predicting the response to neoadjuvant chemotherapy in cervical cancer patients
Yan Hou, Mingzhu Yin, Fengyu Sun, Tao Zhang, Xiaohua Zhou, Huiyan Li, Jian Zheng, Xiuwei Chen, Cong Li, Xiaoming Ning, Ge Lou and Kang Li  
DOI: 10.1039/C4MB00054D

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 
DOI: 10.1039/C3MB25489E

Structure-based virtual screening of novel, high-affinity BRD4 inhibitors
Charuvaka Muvva, E. R. Azhagiya Singam, S. Sundar Raman and V. Subramanian
DOI: 10.1039/C4MB00243A

Trials and tribulations of ‘omics data analysis: assessing quality of SIMCA-based multivariate models using examples from pulmonary medicine
Åsa M. Wheelock and Craig E. Wheelock 
DOI: 10.1039/C3MB70194H

Differential protein profile in sexed bovine semen: shotgun proteomics investigation
Michele De Canio, Alessio Soggiu, Cristian Piras, Luigi Bonizzi, Andrea Galli, Andrea Urbani and Paola Roncada  
DOI: 10.1039/C3MB70306A

Crosstalk between kinases and Nedd4 family ubiquitin ligases
Heeseon An, David T. Krist and Alexander V. Statsyuk 
DOI: 10.1039/C3MB70572B

Mechanism of action-based classification of antibiotics using high-content bacterial image analysis
Kelly C. Peach, Walter M. Bray, Dustin Winslow, Peter F. Linington and Roger G. Linington  
DOI: 10.1039/C3MB70027E

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The name of the game is…game theory!

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

In a review by Bohl and colleagues, which appeared in the August issue of Molecular Biosystems, the principles of game theory are applied to subcellular macromolecules such as RNA, DNA and proteins. The authors recast molecules as “players” who use various strategies to achieve the goals of their host cell/organism, or selfishly, their own goals. We can “consider the result of some mutations or epigenetic modifications as changes in strategy”.

From an evolutionary standpoint the overall goal of an organism is to reproduce. Therefore, any macromolecules that affect reproduction can be considered players. This is especially true of DNA, which can be considered successful if it is able to replicate. Typically we think of genes which persist in a population as beneficial to the host organism, i.e. if a gene were detrimental, that organism would be less likely to reproduce and the gene would disappear from the population. These genes would be said to cooperate in order to promote the success of the carrier organism. However, genes can also act in their own self interest, and be detrimental to the host.

The authors describe three ways for genes to be “selfish”, interference, overreplication and gonotaxis. Interference is the gene preventing the transmission of other genes to the daughter cells, thus increasing its own chances of transmission. The gene can also replicate more than once in a cycle, using overreplication to achieve the same goal. Gonotaxis is more complicated, in that the genes have to avoid being sequestered into non-functional polar bodies during meiosis (see Figs. 1-3 below for diagrams).

InterferenceOverreplication

Gonotaxis

Interestingly, genes that are typically selfish can actually be beneficial in some circumstances. Some bacteria have toxin genes that may have been useful to avoid predators in some circumstances. In the absence of a need for toxin, the cells express “anti-toxin” as a control. Also, jumping genes are sometimes viewed as parasitic because they are usually not crucial to the survival of an organism. However, in the case of arabidopsis, a lack of the “DAYSLEEPER” jumping gene causes growth defects.

Some of the same reason that DNA can be considered players also apply to proteins. For protein complexes in particular the authors consider a game with two players, where the goal is to form a bond. Each protein can be either flexible or rigid. If both are rigid, binding is difficult, and depends on an exact matching of shapes. If both are flexible then binding is easy, but the resulting complex will lack a defined shape. Therefore, the best outcome requires one protein to be rigid, and one to be flexible. This model fits well with recent findings (cited in this paper) of unstructured/disordered regions of proteins which form secondary structure when binding to another protein (induced fit model, see Fig. 4 below).

Induced Fit Binding Model

The ideas of game theory as presented by Bohl et al. are best applied to information encoding macromolecules, such as RNA, DNA and proteins. These principles can be applied to common genetics questions such as “jumping genes”, as well as understanding the activity of disordered proteins.

Evolutionary game theory: molecules as players

Katrin Bohl, Sabine Hummert, Sarah Werner, David Basanta, Andreas Deutsch, Stefan Schuster, Gunter Theißen and Anja Schroeter

Anja Schroeter webpage at Friedrich-Schiller-University Jena (page not in English!)

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Recent HOT Molecular BioSystems articles

The following HOT articles have been highlighted by the reviewers of the articles as being particularly interesting or significant pieces of research. These are all free to access until 31st December 2014. The order they appear in the list has no meaning or ranking.

 Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering
Joris Beld, D. John Lee and Michael D. Burkart  
DOI: 10.1039/C4MB00443D, Review Article

C4MB00443D GA


Studies of N9-arenthenyl purines as novel DFG-in and DFG-out dual Src/Abl inhibitors using 3D-QSAR, docking and molecular dynamics simulations
Shaojie Ma, Guohua Zeng, Danqing Fang, Juping Wang, Wenjuan Wu, Wenguo Xie, Shepei Tan and Kangcheng Zheng  
DOI: 10.1039/C4MB00350K, Paper
C4MB00350K GA

C4MB00457D GA

Identification of cancer-related lncRNAs through integrating genome, regulome and transcriptome features
Tingting Zhao, Jinyuan Xu, Ling Liu, Jing Bai, Chaohan Xu, Yun Xiao, Xia Li and Liming Zhang  
DOI: 10.1039/C4MB00478G, Paper
C4MB00478G GA

UHPLC-LTQ-Orbitrap MS combined with spike-in method for plasma metabonomics analysis of acute myocardial ischemia rats and pretreatment effect of Danqi Tongmai tablet
Bingpeng Yan, Yanping Deng, Jinjun Hou, Qirui Bi, Min Yang, Baohong Jiang, Xuan Liu, Wanying Wu and Dean Guo  
DOI: 10.1039/C4MB00529E, Paper
C4MB00529E GA

A metabolomic and pharmacokinetic study on the mechanism underlying the lipid-lowering effect of orally administered berberine
Shenghua Gu, Bei Cao, Runbin Sun, Yueqing Tang, Janice L. Paletta, Xiao-Lei Wu, Linsheng Liu, Weibin Zha, Chunyan Zhao, Yan Li, Jason M. Radlon, Phillip B. Hylemon, Huiping Zhou, Jiye Aa and Guangji Wang  
DOI: 10.1039/C4MB00500G, Paper

C4MB00500G GA


Modeling the mitotic regulatory network identifies highly efficient anti-cancer drug combinations
Yiran Wu, Xiaolong Zhuo, Ziwei Dai, Xiao Guo, Yao Wang, Chuanmao Zhang and Luhua Lai  
DOI: 10.1039/C4MB00610K, Paper

C4MB00610K GA


Prediction of advanced ovarian cancer recurrence by plasma metabolic profiling
Haiyu Zhang, Tingting Ge, Xiaoming Cui, Yan Hou, Chaofu Ke, Meng Yang, Kai Yang, Jingtao Wang, Bing Guo, Fan Zhang, Ge Lou and Kang Li  
DOI: 10.1039/C4MB00407H, Paper

C4MB00407H GA


A pre-structured helix in the intrinsically disordered 4EBP1
Do-Hyoung Kim, Chewook Lee, Ye-Jin Cho, Si-Hyung Lee, Eun-Ji Cha, Ji-Eun Lim, T. Michael Sabo, Christian Griesinger, Donghan Lee and Kyou-Hoon Han  
DOI: 10.1039/C4MB00532E, Communication

C4MB00532E GA

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