Category: computational biology

Enzyme activity prediction still revolves around the enzyme activity-protein structure correlate

March 29, 2024

From the theoretical perspective, enzyme structure is perhaps the easiest correlate for enzyme activity levels given the intuitive nature of structure-function correlates. But, the challenge lies in extracting useful features from a structural depiction that could be correlated with enzyme activity. To this end, the field of enzyme activity prediction still awaits comprehensive proteome level … More Enzyme activity prediction still revolves around the enzyme activity-protein structure correlate

Cost of synthesis is the main barrier to longer read RNA-sequencing

March 24, 2024

Modern RNA-sequencing relies on next-generation short read sequencing technologies to profile for the total ensemble of mRNA molecules in the sample. Conceptually, it is a formidable challenge as there are literally millions of mRNA molecules that need to be sequenced. The cost of this endeavour is also hefty. To reduce the cost to a manageable … More Cost of synthesis is the main barrier to longer read RNA-sequencing

RNA-seq is a label-free, unbiased genome scale transcriptome profiling technique

March 21, 2024

Understanding gene expression pattern of cells in different health and disease conditions have evolved from an academic curiosity 20 years ago into an almost essential aspect of many biological research workflows. The reason is our newfound ability at correlating gene expression pattern with cellular behaviour and phenotype. To this end, one technique stands out amongst … More RNA-seq is a label-free, unbiased genome scale transcriptome profiling technique

Computational protein design provides insights that enhance our understanding of protein folding principles

March 18, 2024

Structural biology is traditionally an experimental science building on data collected by X-ray crystallography, and more recently, cryo-electron microscopy. Such data and the reconstructed structures provide a lens into the principles of protein folding, and help connect particular protein amino acid sequence, and corresponding solved protein structures. But, solved protein structures are snapshots of a … More Computational protein design provides insights that enhance our understanding of protein folding principles

Reference genome provides genomic loci to align the sequence reads from RNA-seq experiments

February 20, 2024

RNA-seq is a popular and accessible transcriptome profiling method that is increasingly used in biological sciences and medical research. It provides a genome scale unbiased view of the gene expression pattern of the cells and tissues, that help provides a mechanistic perspective to phenotypic behaviour and morphological changes. To analyse such an expansive sequence read … More Reference genome provides genomic loci to align the sequence reads from RNA-seq experiments

Sequence conservation and gene essentiality endow phylogenetic signals in ribosomal proteins

February 13, 2024

Microbes are invisible to the naked eye, and look similar under the microscope where diverse types of microbes could be classified into a few shape categories. Hence, there is a need for other identification and classification methods to catalogue the rich diversity of microbes on Earth. One approach is molecular phylogeny. In molecular phylogeny, the … More Sequence conservation and gene essentiality endow phylogenetic signals in ribosomal proteins

Most microorganisms in the gut microbiota are anaerobic in metabolism

February 11, 2024

Since the Great Oxidation Event billions of years ago, many microbes on Earth live under an aerobic environment, where oxygen serves as the terminal electron acceptor for oxidative phosphorylation. The latter metabolic process is particularly important for harnessing a greater amount of energy from carbon substrates such as glucose compared to anaerobic fermentation. But, the … More Most microorganisms in the gut microbiota are anaerobic in metabolism

Evolution is often a necessary step in metabolic engineering research seeking to implement a new pathway into a species

February 6, 2024

Desire to optimise endogenous cellular metabolism or to prod a microbe to use a new unconventional substrate often requires the implementation of new metabolic pathway in a microbial chassis. While this can be done through a combination of gene overexpression and deletions, the new metabolic pathway often only allows slow growth for the species. This … More Evolution is often a necessary step in metabolic engineering research seeking to implement a new pathway into a species

Cryo-electron microscopy could only output the predominant structure or the structure with the best signal to noise ratio

January 24, 2024

In recent years, cryo-electron microscopy has shown its fortitude in solving an array of increasingly difficult and more complex protein structures. But, is the technique capable of solving all possible conformations of a protein? The answer is no, as cryo-electron microscopy could only output the predominant structure or the structure with the best signal to … More Cryo-electron microscopy could only output the predominant structure or the structure with the best signal to noise ratio

Cryo-electron microscopy is still unable to capture the full motion of an enzyme undergoing catalysis

January 22, 2024

A holy grail in structural biology has been the capturing of movies that depict an enzyme undergoing catalysis, i.e., preferably with the enzyme in motion that captures a substrate, coverts it into a product, and releasing the product. To do so would require a method that could accurately image a protein with high resolution while … More Cryo-electron microscopy is still unable to capture the full motion of an enzyme undergoing catalysis