Welcome to the 10th anniversary issue of Molecular BioSystems
Richard Kelly introduces the 10th anniversary issue of Molecular BioSystems.
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.
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.
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.
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”.
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.
RNAi therapeutics for brain cancer: current advancements in RNAi delivery strategies
Delivering advanced therapies for brain cancer based on RNAi.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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!