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.
What shapes eukaryotic transcriptional bursting?
In this review, we recapitulate how certain molecular aspects of transcription influence transcriptional bursting.
Covalent inhibition of protein tyrosine phosphatases
Chemical strategies for covalent inhibition of protein tyrosine phosphatases.
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.
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.
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.
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.
The development of small-molecule modulators for ClpP protease activity
Deregulating ClpP activity either through inhibition or overactivation could lead to antibacterial activity.
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.
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.
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.
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.
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.
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.
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.
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).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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!