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Themed collection 10th Anniversary of Molecular BioSystems

24 items
Editorial

Welcome to the 10th anniversary issue of Molecular BioSystems

Richard Kelly introduces the 10th anniversary issue of Molecular BioSystems.

Graphical abstract: Welcome to the 10th anniversary issue of Molecular BioSystems
From the themed collection: 10th Anniversary of Molecular BioSystems
Review Article

An analysis of surface proteomics results reveals novel candidates for intracellular/surface moonlighting proteins in bacteria

Dozens of intracellular proteins have a second function on the cell surface, referred to as “intracellular/surface moonlighting proteins”. An analysis of the results of 22 cell surface proteomics studies was performed to address whether the hundreds of intracellular proteins found on the cell surface could be candidates for being additional intracellular/surface moonlighting proteins.

Graphical abstract: An analysis of surface proteomics results reveals novel candidates for intracellular/surface moonlighting proteins in bacteria
From the themed collection: 10th Anniversary of Molecular BioSystems
Review Article

Reconstructing and analysing cellular states, space and time from gene expression profiles of many cells and single cells

Gene expression profiling is a fast, cheap and standardised analysis that provides a high dimensional measurement of the state of a biological sample, including of single cells. Computational methods to reconstruct the composition of samples and spatial and temporal information from expression profiles are described, as well as how they can be used to describe the effects of genetic variation.

Graphical abstract: Reconstructing and analysing cellular states, space and time from gene expression profiles of many cells and single cells
From the themed collection: 10th Anniversary of Molecular BioSystems
Review Article

Next-generation analysis of gene expression regulation – comparing the roles of synthesis and degradation

Technological advances have enabled multi-dimensional analyses of gene expression regulation and its dynamics.

Graphical abstract: Next-generation analysis of gene expression regulation – comparing the roles of synthesis and degradation
From the themed collection: 10th Anniversary of Molecular BioSystems
Review Article

The generation of phosphoserine stretches in phosphoproteins: mechanism and significance

A STRING analysis of proteins containing clusters of 3 or more adjacent phosphoserine residues reveals that the great majority of these proteins are interconnected by physical and/or functional links to generate a kind of “phosphoclusterome”.

Graphical abstract: The generation of phosphoserine stretches in phosphoproteins: mechanism and significance
From the themed collection: 10th Anniversary of Molecular BioSystems
Review Article

Engineering reprogrammable RNA-binding proteins for study and manipulation of the transcriptome

With the expanding interest in RNA biology, interest in artificial RNA-binding proteins (RBPs) is likewise increasing.

Graphical abstract: Engineering reprogrammable RNA-binding proteins for study and manipulation of the transcriptome
From the themed collection: 10th Anniversary of Molecular BioSystems
Review Article

RNAi therapeutics for brain cancer: current advancements in RNAi delivery strategies

Delivering advanced therapies for brain cancer based on RNAi.

Graphical abstract: RNAi therapeutics for brain cancer: current advancements in RNAi delivery strategies
From the themed collection: 10th Anniversary of Molecular BioSystems
Review Article

Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences

With the avalanche of DNA/RNA sequences generated in the post-genomic age, it is urgent to develop automated methods for analyzing the relationship between the sequences and their functions.

Graphical abstract: Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences
From the themed collection: 10th Anniversary of Molecular BioSystems
Review Article

Progress and challenges in predicting protein methylation sites

We review the progress in the prediction of protein methylation sites in the past 10 years and discuss the challenges that are faced while developing novel predictors in the future.

Graphical abstract: Progress and challenges in predicting protein methylation sites
From the themed collection: 10th Anniversary of Molecular BioSystems
Communication

Dihydrofolate reductase inhibitory peptides screened from a structured designed β-loop peptide library displayed on phage

Enzyme inhibitory peptides with a loop structure stabilized using an antiparallel β-sheet scaffold (β-loop peptide) were obtained from a designed peptide phage library.

Graphical abstract: Dihydrofolate reductase inhibitory peptides screened from a structured designed β-loop peptide library displayed on phage
From the themed collection: 10th Anniversary of Molecular BioSystems
Communication

A library approach to rapidly discover photoaffinity probes of the mRNA decapping scavenger enzyme DcpS

A photoaffinity library expedited the discovery of a site-specific DcpS probe.

Graphical abstract: A library approach to rapidly discover photoaffinity probes of the mRNA decapping scavenger enzyme DcpS
From the themed collection: Chemical Biology in Molecular BioSystems
Paper

Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation

While using a serine (S) as linker for circularization increases the thermostability, a longer linker (RGKCWE) leads to reduced aggregation after heat shock at elevated temperatures.

Graphical abstract: Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation
From the themed collection: 10th Anniversary of Molecular BioSystems
Open Access Paper

The transcriptome of Euglena gracilis reveals unexpected metabolic capabilities for carbohydrate and natural product biochemistry

Euglena gracilis is a highly complex green alga. In evolutionary terms is most closely related to the protozoan parasites Trypanosoma and Leishmania but it also shows characteristics of both plants and animals.

Graphical abstract: The transcriptome of Euglena gracilis reveals unexpected metabolic capabilities for carbohydrate and natural product biochemistry
From the themed collection: 10th Anniversary of Molecular BioSystems
Paper

Human genes with a greater number of transcript variants tend to show biological features of housekeeping and essential genes

Human genes with a greater number of transcript variants are more likely to play functionally important roles such as cellular maintenance and survival.

Graphical abstract: Human genes with a greater number of transcript variants tend to show biological features of housekeeping and essential genes
From the themed collection: 10th Anniversary of Molecular BioSystems
Paper

Protein–protein interactions generate hidden feedback and feed-forward loops to trigger bistable switches, oscillations and biphasic dose–responses

Our work reveals that simple reversible protein–protein interactions, when embedded into signalling cascades, give rise to extremely rich and complex regulatory dynamics in the absence of explicit positive and negative feedbacks.

Graphical abstract: Protein–protein interactions generate hidden feedback and feed-forward loops to trigger bistable switches, oscillations and biphasic dose–responses
From the themed collection: 10th Anniversary of Molecular BioSystems
Open Access Paper

Fuzziness endows viral motif-mimicry

The local dynamics of host and viral peptide motifs suggests a different scenario for partner recognition. Host peptide motifs serve as molecular recognition elements, while viral motifs preserve the structural heterogeneity and remain fuzzy when bound to the host.

Graphical abstract: Fuzziness endows viral motif-mimicry
From the themed collection: 10th Anniversary of Molecular BioSystems
Paper

Charting the interactome of PDE3A in human cells using an IBMX based chemical proteomics approach

We characterized a new resin for the enrichment of multiple phosphodiesterases and their interactors.

Graphical abstract: Charting the interactome of PDE3A in human cells using an IBMX based chemical proteomics approach
From the themed collection: 10th Anniversary of Molecular BioSystems
Open Access Paper

Exploration of the HIF-1α/p300 interface using peptide and Adhiron phage display technologies

A range of experimental approaches are used to understand the HIF-1α/p300 interface – an important anticancer drug development target – in greater detail.

Graphical abstract: Exploration of the HIF-1α/p300 interface using peptide and Adhiron phage display technologies
From the themed collection: Chemical Biology in Molecular BioSystems
Paper

Probing the epigenetic regulation of HIF-1α transcription in developing tissue

HIF-1-mediated hypoxia signalling in embryonic tissue is probed by assessing the methylation status of the HIF-1α and EPO HRE promoters using bisulfite sequencing.

Graphical abstract: Probing the epigenetic regulation of HIF-1α transcription in developing tissue
From the themed collection: 10th Anniversary of Molecular BioSystems
Paper

Synthesis of a large library of macrocyclic peptides containing multiple and diverse N-alkylated residues

A large library of macrocyclic peptides containing multiple N-alkylated structures was prepared as one-bead one-compound format.

Graphical abstract: Synthesis of a large library of macrocyclic peptides containing multiple and diverse N-alkylated residues
From the themed collection: Chemical Biology in Molecular BioSystems
Paper

A genetically amenable platensimycin- and platencin-overproducer as a platform for biosynthetic explorations: a showcase of PtmO4, a long-chain acyl-CoA dehydrogenase

Platensimycin and platencin congeners from overproducing strains support PtmO4 as a long-chain acyl-CoA dehydrogenase catalyzing β-oxidation of the diterpenoid intermediates.

Graphical abstract: A genetically amenable platensimycin- and platencin-overproducer as a platform for biosynthetic explorations: a showcase of PtmO4, a long-chain acyl-CoA dehydrogenase
From the themed collection: 10th Anniversary of Molecular BioSystems
Paper

Synthetic small molecules that induce neuronal differentiation in neuroblastoma and fibroblast cells

Imidazole-based synthetic small molecules promote neurogenesis in readily available and simply manageable neuroblastoma and fibroblast cells.

Graphical abstract: Synthetic small molecules that induce neuronal differentiation in neuroblastoma and fibroblast cells
From the themed collection: Chemical Biology in Molecular BioSystems
Paper

Probing the effect of an inhibitor of an ATPase domain of Hsc70 on clathrin-mediated endocytosis

Az blocks the association of Hsc70 with clathrin and consequently suppresses the disassembly of CCVs during clathrin-mediated endocytosis.

Graphical abstract: Probing the effect of an inhibitor of an ATPase domain of Hsc70 on clathrin-mediated endocytosis
From the themed collection: Chemical Biology in Molecular BioSystems
Method

iSBatch: a batch-processing platform for data analysis and exploration of live-cell single-molecule microscopy images and other hierarchical datasets

iSBatch: an ImageJ plugin for fast evaluation of analysis pipelines and visual exploration of datasets.

Graphical abstract: iSBatch: a batch-processing platform for data analysis and exploration of live-cell single-molecule microscopy images and other hierarchical datasets
From the themed collection: 10th Anniversary of Molecular BioSystems
24 items

About this collection

2015 marks the 10th anniversary of Molecular BioSystems.

We would like to thank everyone who has helped us reach this landmark, the many dedicated authors, reviewers and Editorial Board members – all of whom have made Molecular BioSystems what it is today.

This issue celebrates the 10 years that Molecular BioSystems has been published by bringing together research from across the many facets of its scope that we feel exemplifies the kind of high impact science the journal aims to publish.

It has been a great 10 years and we look forward to working alongside everyone working at the chemistry-biology interface for many more to come.

We shall be adding more articles to this collection as they are published so keep checking back for new additions!

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