Unravelling the mechanism of allosteric hepatitis C virus inhibition – a new HOT article

New insights into how the spread of hepatitis C virus (HCV) can be prevented using an enzyme inhibitor have been reported in Molecular BioSystems.

Free and bound protein

Motion modes of the free and bound protein from PCA analysis

Hai-Feng Chen’s group at Shanghai Jiaotong University used molecular dynamics to study the effect of a cyclopropylindolobenzazepine derivative, M2. The technique was used to model just how M2 suppressed a key viral protein, NS5B, to stop the virus from replicating.

M2 is known to be an efficient and highly specific HCV inhibitor. Because the enzyme it targets has no mammalian equivalent, it could be used to fight viral infection without any risk of it adversely affecting any important human enzymes. However, exactly how its inhibition works isn’t yet known.

The group found that when M2 bound to NS5B it caused a conformational change through an allosteric mechanism, changing it from an “open” to a “closed” form. This change destabilised the enzyme, altering information transfer from the substrate binding site to the catalytic domain and drastically weakening its effect. The M2-bound enzyme had greater structural variation – particularly in its A1 loop – indicating its lack of stability.

The allosteric mechanism was confirmed by testing a weakened form of M2, which had significantly less effect on the connectivity of the enzyme than the normal version. A further in vitro resistance study reinforced this by comparing the normal enzyme to a mutant version with a truncated A1 loop. Inhibition of the mutant version was far less effective than that of the wild type, highlighting the importance of the A1 loop in the inhibition mechanism.

Understanding exactly how M2 inhibits viral NS5B, and how mutated forms of the virus might resist this, is vital – it could in future lead to new and more effective drugs to fight HCV.


Read the full article here:

Allosteric mechanism of cyclopropylindolobenzazepine inhibitors for HCV NS5B RdRp via dynamic correlation network analysis
Mueed ur Rahman, Hao Liu, Abdul Wadood and Hai-Feng Chen
Mol. BioSyst., 2016, Advance Article
DOI: 10.1039/C6MB00521G


Susannah May is a guest web writer for the RSC Journal blogs. She currently works in the Publishing Department of the Royal Society of Chemistry, and has a keen interest in biology and biomedicine, and the frontiers of    their intersection with chemistry. She can be found on Twitter using @SusannahCIMay.

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Top 10 Reviewers for Molecular BioSystems

In celebration of Peer Review Week, with the theme around Recognition for Review – we would like to highlight the top 10 reviewers for Molecular BioSystems in 2016, as selected by the editor for their significant contribution to the journal.

Name Institution
Dr Sandipan Chakraborty Indian Association for the Cultivation of Science
Dr Hongtao Zhao Medivir AB
Dr Tong Wang Jinan University
Dr Sheng Wang Toyota Technological Institute at Chicago
Dr Peter Gannett Nova Southeastern University
Dr Wolfgang Fischer National Yang-Ming University
Dr Paola Roncada Istituto Sperimentale Italiano L. Spallanzani
Dr Jun Yin Georgia State University
Dr Jeronimo Lameira Universidade Federal do Pará
Dr Thomas Dandekar University of Würzburg

















We would like to say a massive thank you to these reviewers as well as the Molecular BioSystems Editorial and Advisory Boards and all of the Chemical Biology, -omics and Systems Biology communities for their continued support of the journal, as authors, reviewers and readers.

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What are your colleagues reading in Molecular BioSystems?

The articles below are some of the most read Molecular BioSystems articles in April, May and June 2016.

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

Proteomic analysis of exosomal cargo: the challenge of high purity vesicle isolation
Agata Abramowicz, Piotr Widlak and Monika Pietrowska
DOI: 10.1039/C6MB00082G

Why phosphoproteomics is still a challenge
Fiorella A. Solari, Margherita Dell’Aica, Albert Sickmann and René P. Zahedi
DOI: 10.1039/C5MB00024F

Peptide-tags for site-specific protein labelling in vitro and in vivo
Jonathan Lotze, Ulrike Reinhardt, Oliver Seitz and Annette G. Beck-Sickinger
DOI: 10.1039/C6MB00023A

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

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

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

Elucidating the interaction of limonene with bovine serum albumin: a multi-technique approach
Sumit Kumar Chaturvedi, Ejaz Ahmad, Javed Masood Khan, Parvez Alam, Mohd Ishtikhar and Rizwan Hasan Khan
DOI: 10.1039/C4MB00548A

PLS/OPLS models in metabolomics: the impact of permutation of dataset rows on the K-fold cross-validation quality parameters
Mohamed N. Triba, Laurence Le Moyec, Roland Amathieu, Corentine Goossens, Nadia Bouchemal, Pierre Nahon, Douglas N. Rutledge and Philippe Savarin
DOI: 10.1039/C4MB00414K

The transcriptome of Euglena gracilis reveals unexpected metabolic capabilities for carbohydrate and natural product biochemistry
Ellis C. O’Neill, Martin Trick, Lionel Hill, Martin Rejzek, Renata G. Dusi, Chris J. Hamilton, Paul V. Zimba, Bernard Henrissat and Robert A. Field
DOI: 10.1039/C5MB00319A

Evolutionary game theory: cells as players
Sabine Hummert, Katrin Bohl, David Basanta, Andreas Deutsch, Sarah Werner, Günter Theißen, Anja Schroeter and Stefan Schuster
DOI: 10.1039/C3MB70602H

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

Exploration of the HIF-1α/p300 interface using peptide and Adhiron phage display technologies
Hannah F. Kyle, Kate F. Wickson, Jonathan Stott, George M. Burslem, Alexander L. Breeze, Christian Tiede, Darren C. Tomlinson, Stuart L. Warriner, Adam Nelson, Andrew J. Wilson and Thomas A. Edwards
DOI: 10.1039/C5MB00284B

Next generation sequencing: implications in personalized medicine and pharmacogenomics
Bahareh Rabbani, Hirofumi Nakaoka, Shahin Akhondzadeh, Mustafa Tekin and Nejat Mahdieh
DOI: 10.1039/C6MB00115G

A quinazoline-based HDAC inhibitor affects gene expression pathways involved in cholesterol biosynthesis and mevalonate in prostate cancer cells
Z. Lin, K. S. Bishop, H. Sutherland, G. Marlow, P. Murray, W. A. Denny and L. R. Ferguson
DOI: 10.1039/C5MB00554J

Systems biology analysis of hepatitis C virus infection reveals the role of copy number increases in regions of chromosome 1q in hepatocellular carcinoma metabolism
Ibrahim E. Elsemman, Adil Mardinoglu, Saeed Shoaie, Taysir H. Soliman and Jens Nielsen
DOI: 10.1039/C5MB00827A

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

Evolutionary game theory: molecules as players
Katrin Bohl, Sabine Hummert, Sarah Werner, David Basanta, Andreas Deutsch, Stefan Schuster, Günter Theißen and Anja Schroeter
DOI: 10.1039/C3MB70601J

Metabolomics in diabetic complications
Laura A. Filla and James L. Edwards
DOI: 10.1039/C6MB00014B

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

Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis
Aakash Chavan Ravindranath, Nolen Perualila-Tan, Adetayo Kasim, Georgios Drakakis, Sonia Liggi, Suzanne C. Brewerton, Daniel Mason, Michael J. Bodkin, David A. Evans, Aditya Bhagwat, Willem Talloen, Hinrich W. H. Göhlmann, QSTAR Consortium, Ziv Shkedy and Andreas Bender
DOI: 10.1039/C4MB00328D

The ring residue proline 8 is crucial for the thermal stability of the lasso peptide caulosegnin II
Julian D. Hegemann, Christopher D. Fage, Shaozhou Zhu, Klaus Harms, Francesco Saverio Di Leva, Ettore Novellino, Luciana Marinelli and Mohamed A. Marahiel
DOI: 10.1039/C6MB00081A

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

Comprehensive mapping of O-GlcNAc modification sites using a chemically cleavable tag
Matthew E. Griffin, Elizabeth H. Jensen, Daniel E. Mason, Courtney L. Jenkins, Shannon E. Stone, Eric C. Peters and Linda C. Hsieh-Wilson
DOI: 10.1039/C6MB00138F

A genome-scale metabolic model of Methanococcus maripaludis S2 for CO2 capture and conversion to methane
Nishu Goyal, Hanifah Widiastuti, I. A. Karimi and Zhi Zhou
DOI: 10.1039/C3MB70421A

Keep up-to-date with the latest issues of Molecular BioSystems by joining our E-alerts.

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Unravelling a knotty problem: A simulation study of neurotoxic knotted proteins

Posted on behalf of Susannah May, guest web writer for Molecular BioSystems

Knotted proteins and their part in neurodegenerative diseases such as Huntington’s and spinal muscular atrophy have been put under scrutiny in a new HOT article recently published in Molecular Biosystems.

Two example trajectories that lead to the translocation of knotted species (yellow). Left: translocation of 1J85 when pulled in the I-N protocol. Right: unfolding of a HTT60 knotted conformation (polyQ part = red).

It’s long been known that aggregations of certain proteins have a key role in many neurodegenerative diseases, including Alzheimer’s, Parkinson’s and Huntington’s. However, exactly how these aggregations happen and how it causes disease is still a subject of intense study.

Marek Cieplak’s group at the Polish University of Sciences have used mathematical simulations to study this still-mysterious phenomenon. They looked at huntingtin, a protein involved in embryonic development. If this protein mutates, it can cause neurodegenerative diseases such as Huntington’s by forming toxic oligomers and amyloid fibres. Recent evidence has suggested that monomer forms of the protein could also be neurotoxic – Cieplak’s group theorise that this is due to knots in the structure of the protein that prevent neurodegeneration by the proteasome.

The group used mathematical simulations to create theoretical models of the knotted protein and the proteasome, and investigated the effect that the former would have on the latter under different conditions of force. Their results point to the knots being responsible for the jamming of the proteasome’s degradation mechanism. Under certain conditions proteins would stay knotted instead of untying, hindering normal neurodegeneration and leading to neurotoxic build-up of proteins.

The results will help to provide greater understanding of the mechanisms behind genetic diseases such as Huntington’s, paving the way for future experimental studies and, hopefully one day, the development of new and effective treatments.


Read the full article here:

Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteins
Michał Wojciechowski, Àngel Gómez-Sicilia, Mariano Carrión-Vázquez and Marek Cieplak
DOI: 10.1039/C6MB00214E




Susannah May is a guest web writer for the RSC Journal blogs. She currently works in the Publishing Department of the Royal Society of Chemistry, and has a keen interest in biology and biomedicine, and the frontiers of their intersection with chemistry. She can be found on Twitter using @SusannahCIMay.

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‘Microbial protein targets: towards understanding and intervention’ meeting

Hosted by The British Society of Parasitology in collaboration with the Royal Society of Chemistry

Microbial protein targets: towards understanding and intervention

14–16 September 2016, Durham, UK

This symposium will bring together leading expertise in protein structure determination, biochemical characterization and chemical biology to explore the most recent advances in the understanding of protein function and inhibition in microbial pathogens – both bacteria and parasites.

An exciting line-up of speakers will present their recent work in the area. Some of the confirmed speakers are:

  • Chris Abell University of Cambridge, UK
  • Gerald Spaeth Institut Pasteur, Paris, France
  • Ed Tate Imperial College London, UK
  • Maria Marco-Martin GSK Tres Contos, Spain

Take advantage of this opportunity to showcase your work alongside leaders in the field and submit an abstract for an oral or poster presentation today. Through generous sponsorship from the RSC Chemical Biology Interface Division and the BSP there are bursaries available for early career researchers to support their participation at this meeting.

The oral abstract deadline has just been extended until 15 July 2016, and poster abstracts are welcome until 5 August 2016. For more information and to register please visit the conference webpage.

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11th annual meeting of the Japanese Society for Chemical Biology

The 11th annual meeting of the Japanese Society for Chemical Biology was held in Kyoto, Japan from the 15 – 17th June 2016.  Molecular BioSystems was pleased to award two poster prizes.

Congratulations to the winners:

Dr. Mizuki Endo (University of Tokyo): Light-induced protein oligomerization system for the optogenetic control of neurite outgrowth direction in living animal

Mr. Kazuma Mori (Osaka University): Clarification the Function of GLUT4 N-glycan in the Intracellular Trafficking Based on PYP-tag Technology and New Long-wavelength Fluorescent Probes

The winners were presented with their prizes by committe chair Prof. Hiroshi Sugiyama (Kyoto University).

Prof Sugiyama (left) presents Dr. Mizuki Endo (right) with his prize

Mr. Kazuma Mori (far left) and Prof. Hiroshi Sugiyama (far right)

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What are your colleagues reading in Molecular BioSystems?

The articles below are some of the most read Molecular BioSystems articles in January, February and March 2016.

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, Review Article

Why phosphoproteomics is still a challenge
Fiorella A. Solari, Margherita Dell’Aica, Albert Sickmann and René P. Zahedi
DOI: 10.1039/C5MB00024F, Opinion

Exploration of the HIF-1α/p300 interface using peptide and Adhiron phage display technologies
Hannah F. Kyle, Kate F. Wickson, Jonathan Stott, George M. Burslem, Alexander L. Breeze, Christian Tiede, Darren C. Tomlinson, Stuart L. Warriner, Adam Nelson, Andrew J. Wilson and Thomas A. Edwards
DOI: 10.1039/C5MB00284B, Paper

PLS/OPLS models in metabolomics: the impact of permutation of dataset rows on the K-fold cross-validation quality parameters
Mohamed N. Triba, Laurence Le Moyec, Roland Amathieu, Corentine Goossens, Nadia Bouchemal, Pierre Nahon, Douglas N. Rutledge and Philippe Savarin
DOI: 10.1039/C4MB00414K, Opinion

The PI3K/AKT/mTOR interactive pathway
Tulin Ersahin, Nurcan Tuncbag and Rengul Cetin-Atalay
DOI: 10.1039/C5MB00101C, Paper

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, Opinion

The transcriptome of Euglena gracilis reveals unexpected metabolic capabilities for carbohydrate and natural product biochemistry
Ellis C. O’Neill, Martin Trick, Lionel Hill, Martin Rejzek, Renata G. Dusi, Chris J. Hamilton, Paul V. Zimba, Bernard Henrissat and Robert A. Field
DOI: 10.1039/C5MB00319A, Paper

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, Review Article

Metabolomic analysis of riboswitch containing E. coli recombinant expression system
Howbeer Muhamadali, Yun Xu, Rosa Morra, Drupad K. Trivedi, Nicholas J. W. Rattray, Neil Dixon and Royston Goodacre
DOI: 10.1039/C5MB00624D, Paper

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, Paper

Read more »

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Bacterial identification gets a culture shock

Written for Chemistry World

Scientists in the UK have developed a new tool to distinguish bacterial strains from each other. This speedy method could help to minimise drug resistance by accurately directing antibiotic treatment at an early stage.

Antimicrobial resistance is a major health concern and its risk is growing evermore due to a lack of both new drugs and rapid point-of-care diagnostic tools to ensure best use of the drugs in hand. ‘Innovative solutions to identifying pathogens can be found – which is really needed as antibiotic resistance spreads – if different fields work together,’ explains Matthew Gibson from the University of Warwick, whose group developed the new diagnostic tool.

Current point-of-care methods to identify bacteria require culturing bacteria to grow them to higher density – a very slow process. New sequencing technologies are faster, but still require hours and special equipment. Gibson’s method makes use of adhesion between bacteria and other cells. Many bacteria bind to cells through protein or carbohydrate structures exposed on the surface of the bacterium called adhesins. Each bacterial strain has a very specific pattern of adhesins and therefore binds with different strength to different sugar-bearing cell surfaces.


Read the full story in Chemistry World


Read the original journal article in Molecular BioSystems – it is open access.

Discrimination between bacterial species by ratiometric analysis of their carbohydrate binding profile
L. Otten, E. Fullam and M. I. Gibson, Mol. Biosyst., 2016, Advance Article
DOI: 10.1039/C5MB00720H, Communication

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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 2015.

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, Review Article

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, Review Article

Why phosphoproteomics is still a challenge
Fiorella A. Solari, Margherita Dell’Aica, Albert Sickmann and René P. Zahedi
DOI: 10.1039/C5MB00024F, Opinion

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

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, Paper

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, Paper

Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis
Aakash Chavan Ravindranath, Nolen Perualila-Tan, Adetayo Kasim, Georgios Drakakis, Sonia Liggi, Suzanne C. Brewerton, Daniel Mason, Michael J. Bodkin, David A. Evans, Aditya Bhagwat, Willem Talloen, Hinrich W. H. Göhlmann, QSTAR Consortium, Ziv Shkedy and Andreas Bender
DOI: 10.1039/C4MB00328D, Paper

NMR- and MS-based metabolomics: various organ responses following naphthalene intervention
Yee Soon Ling, Hao-Jan Liang, Meng-Hsuan Chung, Ming-Huan Lin and Ching-Yu Lin
DOI: 10.1039/C4MB00090K, Paper

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
DOI: 10.1039/B500266D, Paper

Development of novel assays for lignin degradation: comparative analysis of bacterial and fungal lignin degraders
Mark Ahmad, Charles R. Taylor, David Pink, Kerry Burton, Daniel Eastwood, Gary D. Bending and Timothy D. H. Bugg
DOI: 10.1039/B908966G, Paper

Read more »

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2016 RSC Prizes and Awards in Organic Chemistry & Chemical Biology now open for nomination

Nominate someone you know who is an exceptional talent in chemical sciences

The 2016 RSC Prizes and Awards are now open for nomination!

Nominations will close on 15 January 2016.


For more than 140 years, our Prizes and Awards programme has been acknowledging and celebrating exceptional talent in the chemical sciences, and with your support we are hoping that 2016 will even more successful!

Last year’s winners include Chemists such as Prof. Wilfred van der Donk (University of Illinois), Prof. Tim Donohoe (University of Oxford), Prof. Shuli You (Shanghai Institute of Organic Chemistry), Prof. Philip Gale (University of Southampton), Prof. Herman Overkleeft (Leiden University), Prof. Alison Ashcroft and Prof. Sheena Radford (University of Leeds).

This year we have 63 prizes and awards open for nominations of individuals, teams and organisations covering the breadth of the chemical sciences across academia, education and industry.

This year’s prizes in the field of Organic Chemistry & Chemical Biology include:

CBID (Chemistry Biology Interface Division) awards –

Organic Awards –

For 2016 our Longstaff Prize is also open – since 1881 we have awarded this prize once every three years to one of our members who has achieved the most to advance the science of chemistry.

Submit your suggestions now!

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