Archive for the ‘Hot Articles’ Category

Recent HOT Molecular BioSystems articles

Understanding and applying tyrosine biochemical diversity
Lyn H. Jones, Arjun Narayanan and Erik C. Hett  
Mol. BioSyst., 2014,10, 952-969
DOI: 10.1039/C4MB00018H

Understanding and applying tyrosine biochemical diversity

Free to access until 7th May 2014


Cell growth and protein expression of Shewanella oneidensis in biofilms and hydrogel-entrapped cultures
Yingdan Zhang, Chun Kiat Ng, Yehuda Cohen and Bin Cao
Mol. BioSyst., 2014,10, 1035-1042
DOI: 10.1039/C3MB70520J

Cell growth and protein expression of Shewanella oneidensis in biofilms and hydrogel-entrapped cultures

Free to access until 7th May 2014


Quantitative phosphoproteomic profiling of PINK1-deficient cells identifies phosphorylation changes in nuclear proteins
Xiaoyan Qin, Chaoya Zheng, John R. Yates III and Lujian Liao  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70565J

Quantitative phosphoproteomic profiling of PINK1-deficient cells identifies phosphorylation changes in nuclear proteins

Free to access until 7th May 2014


Regulation of cell survival by the HIP-55 signaling network
Chengzhi Yang, Zenggang Li, Zhi Shi, Kangmin He, Aiju Tian, Jimin Wu, Youyi Zhang and Zijian Li  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70552H

Regulation of cell survival by the HIP-55 signaling network

Free to access until 7th May 2014


Prioritization of candidate disease genes by enlarging the seed set and fusing information of the network topology and gene expression
Shao-Wu Zhang, Dong-Dong Shao, Song-Yao Zhang and Yi-Bin Wang
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70588A

Prioritization of candidate disease genes by enlarging the seed set and fusing information of the network topology and gene expression

 

Free to access until 7th May 2014

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Free access to HOT articles

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

A novel network pharmacology approach to analyse traditional herbal formulae: the Liu-Wei-Di-Huang pill as a case study
Xujun Liang, Huiying Li and Shao Li  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70507B, Paper

Graphical abstract: A novel network pharmacology approach to analyse traditional herbal formulae: the Liu-Wei-Di-Huang pill as a case study

A comprehensive analysis of the Streptococcus pyogenes and human plasma protein interaction network
Kristoffer Sjöholm, Christofer Karlsson, Adam Linder and Johan Malmström  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70555B, Paper

Graphical abstract: A comprehensive analysis of the Streptococcus pyogenes and human plasma protein interaction network

Engineering reduced evolutionary potential for synthetic biology
Brian A. Renda, Michael J. Hammerling and Jeffrey E. Barrick  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70606K, Review Article

Graphical abstract: Engineering reduced evolutionary potential for synthetic biology

Structure-based engineering and comparison of novel split inteins for protein ligation
A. Sesilja Aranko, Jesper S. Oeemig, Dongwen Zhou, Tommi Kajander, Alexander Wlodawer and Hideo Iwaï  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C4MB00021H, Paper

Graphical abstract: Structure-based engineering and comparison of novel split inteins for protein ligation
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Fibrils, oligomers or just precursors? New probe characterises beta-amyloid aggregates

Beta-amyloid (Aβ) aggregates are infamous for forming the toxic plaques in the brain of Alzheimer’s disease patients. The detrimental effects are fairly well studied, but the mechanism of formation remains largely a mystery.

Now, thanks to Ifor D. W. Samuel, J. Carlos Penedo and colleagues at University of St. Andrews and Glasgow University, researchers have a new fluorescent probe to study the process of Aβ aggregation. This paper was featured on the cover of the January 2014 issue of Molecular Biosystems.


The most common probe of Aβ currently in use is Thioflavin T (ThT), which has been very successful at detecting the presence of aggregates. However, this probe has a limited pH range where it can be used. Aggregate structures can form at low concentrations of Aβ, and in the slightly acidic (pH = 6) endosome, but both of these are beyond the detection limits of ThT. For maximum utility, a probe would be able to track Aβ formation under any biological conditions.

Fig 1: Representative aggregation time course and relative fluorescence quenching during the HFIP-induced aggregation of Ab1–42

To address this disadvantage, Samuel & Penedo et al. have used a HiLyte Fluorescent probe attached to the N-terminal position of Aβ monomers. When monomers associate with each other, the probe undergoes fluorescence self-quenching (FSQ), a well-documented process where the presence of two probes proximal to each other will cause a decrease in the observed fluorescent signal. This decrease in signal can be monitored and correlated with the aggregation rate and type of Aβ structure formed.

First the researchers determined that the probe did not affect the final Aβstructures obtained by a TEM image comparison to ThT Aβ under various conditions (see Figure 1 below). They also showed that the rate of Aβ formation stayed the same. Because the HiLyte probe does not affect the normal Aβ function, they could then use the probe under biological conditions not accessible to ThT.

They found that they were able to detect fibrils under biological conditions (Figure 2a below), oligomers under endosomal conditions (Figure 2bbelow) and ADDLs (early precursor structures that occur at low Aβ concentrations). Each of these Aβ structures produced a different fluorescent signature, allowing them to be distinguished from each other. This ability to detect the different Aβ assembly rates will allow researchers to better characterize biological samples, hopefully leading to new treatment options for Alzheimer’s disease.

Fig 2: (a,b) Transmission electron micrographs of negatively stained Ab555


Read Samuel & Penedo et al’s HOT paper by following the link below!

DOI: 10.1039/C3MB70272C

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

A metabolomics investigation into the effects of HIV protease inhibitors on HPV16 E6 expressing cervical carcinoma cells
Dong-Hyun Kim, J. William Allwood, Rowan E. Moore, Emma Marsden-Edwards, Warwick B. Dunn, Yun Xu, Lynne Hampson, Ian N. Hampson and Royston Goodacre  
Mol. BioSyst., 2014,10, 398-411
DOI: 10.1039/C3MB70423H, Paper

E88, a new cyclic-di-GMP class I riboswitch aptamer from Clostridium tetani, has a similar fold to the prototypical class I riboswitch, Vc2, but differentially binds to c-di-GMP analogs
Yiling Luo, Bin Chen, Jie Zhou, Herman O. Sintim and T. Kwaku Dayie  
Mol. BioSyst., 2014,10, 384-390
DOI: 10.1039/C3MB70467J, Paper

An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis
Min Zhao, Eric D. Austin, Anna R. Hemnes, James E. Loyd and Zhongming Zhao  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70496C, Paper

Hyperdiploid tumor cells increase phenotypic heterogeneity within Glioblastoma tumors
Prudence Donovan, Kathleen Cato, Roxane Legaie, Rumal Jayalath, Gemma Olsson, Bruce Hall, Sarah Olson, Samuel Boros, Brent A. Reynolds and Angus Harding  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70484J, Paper

Paxillin suppresses the proliferation of HPS rat serum treated PASMCs by up-regulating the expression of cytoskeletal proteins
Yang Chen, Bin Yi, Zhi Wang, Jianteng Gu, Yongshuai Li, Jian Cui and Kaizhi Lu  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70391F, Paper

Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange
Ralf Beer, Konrad Herbst, Nikolaos Ignatiadis, Ilia Kats, Lorenz Adlung, Hannah Meyer, Dominik Niopek, Tania Christiansen, Fanny Georgi, Nils Kurzawa, Johanna Meichsner, Sophie Rabe, Anja Riedel, Joshua Sachs, Julia Schessner, Florian Schmidt, Philipp Walch, Katharina Niopek, Tim Heinemann, Roland Eils and Barbara Di Ventura  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70594C, Paper

A systematic study of chemogenomics of carbohydrates
Jiangyong Gu, Fang Luo, Lirong Chen, Gu Yuan and Xiaojie Xu  
Mol. BioSyst., 2014,10, 391-397
DOI: 10.1039/C3MB70534J, Paper 

The ubiquitin system: an essential component to unlocking the secrets of malaria parasite biology
Michael J. Hamilton, Michael Lee and Karine G. Le Roch  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70506D, Review Article

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Mathematical model takes on the gene expression pathway responsible for whooping cough infections

Dr. Saini and colleague at the Indian Institute of Technology, Bombay have used a mathematical model to track the gene expression pathway of a bacterium that causes whooping cough (or pertussis). The understanding of gene regulation along the growth and infection process for Bordetella could lead to new ways to block its action.

The Bordetella bacterium colonizes the respiratory tracts of several hosts, including humans, to cause the infection most commonly referred to as whooping cough. There are two stages of the infection, with the first being mild (cold like symptoms), followed by the intense coughing and difficulty breathing which creates the characteristic “whooping” sound for which the infection is named. This second stage of the infection is controlled by a specific set of genes in the bacterium DNA, and regulated by one pathway known as BvgAS.

This pathway BvgAS is a series of three phosphorylation reactions, where a phosphate group is added to specific proteins in turn, and the final protein then activates the genes responsible for virulence (infection). The addition or removal of a phosphate group is a standard way for cells to turn proteins “on” or “off” as needed. Figure 1 below shows the activation pathway of the final protein in the series (BvgA, triangle), which is the gene promoter.

Figure 1

The researchers were able to recover experimentally observed gene activation for four important classes of genes. They monitored where the pathway of interest changes from a repressed state (i.e. genes are inactive, or unexpressed), to an intermediate state, and finally to an active state (i.e. genes are expressed). The expression levels for each class of genes observed during the transitions are shown in Fig. 2 below.

Additionally, the same simulations were carried out on mutant bacteria containing one phosphorylation event in the pathway. This was done to understand the role of having three phosphorylation reactions for BvgAS, while typical pathways in bacteria have one or two events. This extra complexity was found to provide the bacterium with sensitivity and flexibility to respond to environmental factors, by changing the gene expression profile.

Understanding how the bacterium can respond to changing environmental factors by regulating gene expression could lead to new treatments for the infection in humans.

Figure 2






Read the full HOT paper by Mahendra Kumar Prajapa and Supreet Saini here:

Role of feedback and network architecture in controlling virulence gene expression in Bordetella, DOI: 10.1039/C3MB70213H

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Free access to HOT articles!

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

Real-time probing of β-amyloid self-assembly and inhibition using fluorescence self-quenching between neighbouring dyes
Steven D. Quinn, Paul A. Dalgarno, Ryan T. Cameron, Gordon J. Hedley, Christian Hacker, John M. Lucocq, George S. Baillie, Ifor D. W. Samuel and J. Carlos Penedo  
Mol. BioSyst., 2014,10, 34-44
DOI: 10.1039/C3MB70272C, Paper

Graphical abstract: Real-time probing of β-amyloid self-assembly and inhibition using fluorescence self-quenching between neighbouring dyes
Integrated analysis of the Wnt responsive proteome in human cells reveals diverse and cell-type specific networks
J. Song, Z. Wang and R. M. Ewing  
Mol. BioSyst., 2014,10, 45-53
DOI: 10.1039/C3MB70417C, Paper

Graphical abstract: Integrated analysis of the Wnt responsive proteome in human cells reveals diverse and cell-type specific networks
On the catalytic mechanism of polysaccharide lyases: evidence of His and Tyr involvement in heparin lysis by heparinase I and the role of Ca2+
Carolina R. Córdula, Marcelo A. Lima, Samuel K. Shinjo, Tarsis F. Gesteira, Laércio Pol-Fachin, Vivien J. Coulson-Thomas, Hugo Verli, Edwin A. Yates, Timothy R. Rudd, Maria A. S. Pinhal, Leny Toma, Carl P. Dietrich, Helena B. Nader and Ivarne L. S. Tersariol  
Mol. BioSyst., 2014,10, 54-64
DOI: 10.1039/C3MB70370C, Paper

Graphical abstract: On the catalytic mechanism of polysaccharide lyases: evidence of His and Tyr involvement in heparin lysis by heparinase I and the role of Ca2+

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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

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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

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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

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Free to access HOT articles in May

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

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


Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes
Alexander E. Lobkovsky, Yuri I. Wolf and Eugene V. Koonin 
DOI: 10.1039/C3MB25553K

 


A study of Caenorhabditis elegans DAF-2 mutants by metabolomics and differential correlation networks
Cecilia Castro, Jan Krumsiek, Nicolas J. Lehrbach, Steven A. Murfitt, Eric A. Miska and Julian L. Griffin
DOI: 10.1039/C3MB25539E


A comprehensive analysis of the influence of drug binding kinetics on drug action at molecular and systems levels
Ning Yin, Jianfeng Pei and Luhua Lai
DOI: 10.1039/C3MB25471B

 


DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle
Patrick Sobetzko, Monika Glinkowska, Andrew Travers and Georgi Muskhelishvili 
DOI: 10.1039/C3MB25515H

 


Proteomic and ionomic profiling reveals significant alterations of protein expression and calcium homeostasis in cystic fibrosis cells
Domenico Ciavardelli, Melania D’Orazio, Luisa Pieroni, Ada Consalvo, Claudia Rossi, Paolo Sacchetta, Carmine Di Ilio, Andrea Battistoni and Andrea Urbani 
DOI: 10.1039/C3MB25594H

 


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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