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Themed collection 2017 Hot Articles in Molecular Biosystems

31 items
Opinion

Diversity of nature's assembly lines – recent discoveries in non-ribosomal peptide synthesis

Highlighting recent important discoveries from the biosynthesis of peptides by linear non-ribosomal peptide synthetase (NRPS) machineries.

Graphical abstract: Diversity of nature's assembly lines – recent discoveries in non-ribosomal peptide synthesis
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Review Article

What shapes eukaryotic transcriptional bursting?

In this review, we recapitulate how certain molecular aspects of transcription influence transcriptional bursting.

Graphical abstract: What shapes eukaryotic transcriptional bursting?
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Review Article

Covalent inhibition of protein tyrosine phosphatases

Chemical strategies for covalent inhibition of protein tyrosine phosphatases.

Graphical abstract: Covalent inhibition of protein tyrosine phosphatases
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Review Article

Emergent properties of extracellular vesicles: a holistic approach to decode the complexity of intercellular communication networks

Holistic approaches to decode emergent properties of extracellular vesicles either at a single vesicle level or at a systems level.

Graphical abstract: Emergent properties of extracellular vesicles: a holistic approach to decode the complexity of intercellular communication networks
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Review Article

Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines

Post-translational modifications on protein cysteines play a crucial role in redox signaling, in the regulation of enzymatic activity and protein function, and in maintaining redox homeostasis in living systems.

Graphical abstract: Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Review Article

Screening methods for identifying pharmacological chaperones

This review highlights recent screening methods for identifying pharmacological chaperones, which are small-molecules capable of rescuing misfolded proteins.

Graphical abstract: Screening methods for identifying pharmacological chaperones
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Review Article

The emerging picture of CDK9/P-TEFb: more than 20 years of advances since PITALRE

CDK9 is a prominent member of the transcriptional CDKs subfamily, a group of kinases whose function is to control the primary steps of mRNA synthesis and processing by eukaryotic RNA polymerase II.

Graphical abstract: The emerging picture of CDK9/P-TEFb: more than 20 years of advances since PITALRE
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Review Article

The development of small-molecule modulators for ClpP protease activity

Deregulating ClpP activity either through inhibition or overactivation could lead to antibacterial activity.

Graphical abstract: The development of small-molecule modulators for ClpP protease activity
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Open Access Communication

DNA condensation in live E. coli provides evidence for transertion

Fluorescence microscopy has been used to examine the condensation of DNA in live bacteria by a tetranuclear polypyridylruthenium(II) complex.

Graphical abstract: DNA condensation in live E. coli provides evidence for transertion
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Fragile X mental retardation protein recognizes a G quadruplex structure within the survival motor neuron domain containing 1 mRNA 5′-UTR

SMNDC1 mRNA adopts a 5′-UTR G quadruplex structure recognized specifically by FMRP, potentially affecting spliceosome assembly in FXS.

Graphical abstract: Fragile X mental retardation protein recognizes a G quadruplex structure within the survival motor neuron domain containing 1 mRNA 5′-UTR
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Dissecting binding of a β-barrel membrane protein by phage display

Membrane proteins (MPs) contribute to a myriad of cellular functions. Phage-display of the TonB dependent transporter and MP, ShuA, allows its rapid mutagenesis for structure-function studies.

Graphical abstract: Dissecting binding of a β-barrel membrane protein by phage display
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Ligand-induced conformational preorganization of loops of c-MYC G-quadruplex DNA and its implications in structure-specific drug design

Ligand binding to c-MYC G-quadruplex DNA induces conformational changes in the loops of the quadruplex. c-MYC quadruplex-specific small molecules can be designed by targeting these loop conformers.

Graphical abstract: Ligand-induced conformational preorganization of loops of c-MYC G-quadruplex DNA and its implications in structure-specific drug design
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Predicting protein–protein interactions from protein sequences by a stacked sparse autoencoder deep neural network

Protein–protein interactions (PPIs) play an important role in most of the biological processes.

Graphical abstract: Predicting protein–protein interactions from protein sequences by a stacked sparse autoencoder deep neural network
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Mathematical modeling reveals differential regulation of MAPK activity by phosphatase proteins in the yeast pheromone response pathway

To prevent indefinite cellular responses to external signals, cells utilize various adaptation mechanisms.

Graphical abstract: Mathematical modeling reveals differential regulation of MAPK activity by phosphatase proteins in the yeast pheromone response pathway
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Dynamic properties of the growth hormone releasing hormone receptor (GHRHR) and molecular determinants of GHRH binding

Dynamic properties of the growth hormone releasing hormone receptor (GHRHR) and molecular determinants of GHRH binding.

Graphical abstract: Dynamic properties of the growth hormone releasing hormone receptor (GHRHR) and molecular determinants of GHRH binding
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Proteomic analysis of prognostic plasma biomarkers in peripheral arterial occlusive disease

A comprehensive patient-based plasma proteomic approach for the identification of potential plasma biomarkers for the screening and detection of good/poor prognosis of peripheral arterial occlusive disease (PAOD).

Graphical abstract: Proteomic analysis of prognostic plasma biomarkers in peripheral arterial occlusive disease
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

GeneSPIDER – gene regulatory network inference benchmarking with controlled network and data properties

A key question in network inference, that has not been properly answered, is what accuracy can be expected for a given biological dataset and inference method.

Graphical abstract: GeneSPIDER – gene regulatory network inference benchmarking with controlled network and data properties
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

The multi-output incoherent feedforward loop constituted by the transcriptional regulators LasR and RsaL confers robustness to a subset of quorum sensing genes in Pseudomonas aeruginosa

The las multi-output IFFL-1 splits the QS regulon into two distinct sub-regulons with different robustness with respect to LasR fluctuations.

Graphical abstract: The multi-output incoherent feedforward loop constituted by the transcriptional regulators LasR and RsaL confers robustness to a subset of quorum sensing genes in Pseudomonas aeruginosa
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

New insights into polyene macrolide biosynthesis in Couchioplanes caeruleus

Analysis of 67–121 biosynthesis reveals how aromatic heptaene producers impose double bond geometry and avoid interference with folate biosynthesis.

Graphical abstract: New insights into polyene macrolide biosynthesis in Couchioplanes caeruleus
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Predicting protein lysine phosphoglycerylation sites by hybridizing many sequence based features

PhoglyPred is an algorithm that can computationally predict protein phosphoglycerylation sites using three different kinds of descriptors.

Graphical abstract: Predicting protein lysine phosphoglycerylation sites by hybridizing many sequence based features
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Cancerous perturbations within the ERK, PI3K/Akt, and Wnt/β-catenin signaling network constitutively activate inter-pathway positive feedback loops

Perturbations in molecular signaling pathways result in a constitutively activated state, leading to malignant transformation of cells.

Graphical abstract: Cancerous perturbations within the ERK, PI3K/Akt, and Wnt/β-catenin signaling network constitutively activate inter-pathway positive feedback loops
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Open Access Paper

The nature of the conserved basic amino acid sequences found among 437 heparin binding proteins determined by network analysis

Heparin/HS binding sites on proteins are composed of manifold small and flexible, basic amino acid sequences, that occur in many members of the proteome.

Graphical abstract: The nature of the conserved basic amino acid sequences found among 437 heparin binding proteins determined by network analysis
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Metabolic profiling study of shikonin's cytotoxic activity in the Huh7 human hepatoma cell line

Metabolic profiling employed for the first time on Huh7 cells upon treatment with shikonin could provide insight into the metabolic perturbations induced by shikonin.

Graphical abstract: Metabolic profiling study of shikonin's cytotoxic activity in the Huh7 human hepatoma cell line
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Environmental factors and risk of aggressive prostate cancer among a population of New Zealand men – a genotypic approach

Genes with SNPs that were significantly associated with risk for aggressive and non-aggressive prostate cancer were identified.

Graphical abstract: Environmental factors and risk of aggressive prostate cancer among a population of New Zealand men – a genotypic approach
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Regulation of lipids is central to replicative senescence

In this work, we show that lipids are highly regulated at transcriptome and metabolite level during replicative senescence.

Graphical abstract: Regulation of lipids is central to replicative senescence
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Identification of novel inhibitors of the translationally controlled tumor protein (TCTP): insights from molecular dynamics

The translationally controlled tumor protein (TCTP) is a highly conserved multifunctional protein, preferentially expressed in mitotically active tissues and is a potential biomarker and a therapeutic target for lung cancers.

Graphical abstract: Identification of novel inhibitors of the translationally controlled tumor protein (TCTP): insights from molecular dynamics
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

The DNA target determines the dimerization partner selected by bHLHZ-like hybrid proteins AhRJun and ArntFos

The molecular basis of protein–partner selection and DNA binding of the basic helix–loop–helix (bHLH) and basic region-leucine zipper (bZIP) superfamilies of dimeric transcription factors is fundamental toward understanding gene regulation.

Graphical abstract: The DNA target determines the dimerization partner selected by bHLHZ-like hybrid proteins AhRJun and ArntFos
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Inference of cancer mechanisms through computational systems analysis

The proposed method correctly identified and accurately quantified primary enzymatic alterations in cancer, and these account for over 80% of the metabolic alterations in the investigated carcinoma.

Graphical abstract: Inference of cancer mechanisms through computational systems analysis
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Biochemical effects of venlafaxine on astrocytes as revealed by 1H NMR-based metabolic profiling

As a serotonin–norepinephrine reuptake inhibitor [SNRI], venlafaxine is one of the most commonly prescribed clinical antidepressants, with a broad range of antidepressant effects.

Graphical abstract: Biochemical effects of venlafaxine on astrocytes as revealed by 1H NMR-based metabolic profiling
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Paper

Altered levels of circulating cytokines and microRNAs in lean and obese individuals with prediabetes and type 2 diabetes

Today obesity and type 2 diabetes (T2D) have both reached epidemic proportions.

Graphical abstract: Altered levels of circulating cytokines and microRNAs in lean and obese individuals with prediabetes and type 2 diabetes
From the themed collection: 2017 Hot Articles in Molecular Biosystems
Open Access Paper

Proteomics profiling of interactome dynamics by colocalisation analysis (COLA)

A combined proteomics and bioinformatics strategy for mapping interactome dynamics via assessment of subcellular protein–protein colocalisations.

Graphical abstract: Proteomics profiling of interactome dynamics by colocalisation analysis (COLA)
From the themed collection: 2017 Hot Articles in Molecular Biosystems
31 items

About this collection

This on-going collection features all the articles published in Molecular Biosystems in 2017 that were highlighted by the reviewers of these articles as being interested or having particularly significant research.

Congratulations to all the authors whose articles are featured!

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