Functional Evolution of Proteins

LP30K protein manifested in hemocytes of Bombyx mori larva on Nosema bombycis infection and showed functional evolution based on glucose- binding domain

Infection by microsporidian Nosema bombycis induced appearance of exclusive protein conjugate of 190 kDa in hemocytes of silkworm Bombyx mori L (Lepidoptera: Bombycidae). Mass spectrometry of the band showed peptides of low molecular weight 30 kDa lipoprotein (LP30K). Six accessions of LP30K identified from the hemocytes comprised 30 K lipoprotein 1, 30 K protein 1, 2, 6, 7 and 11. Two uncharacterised proteins (UCP) identified from the hemocytes showed 100% similarity with LP30K sequence, altogether showed abundance after the infection. The LP30K accessions H9J4F6 (Q00802), E5EVW2 and the UCP accessions D4QGC0 and D4QGB9 showed presence of glucose binding protein I domain "ADSDVPNDILEEQLYNSIVVADYDSAVEK" that binds with fungal glucans to inhibit infection. However glucose binding protein II domain "TLAPRTDDVLAEQLYMSVVIGEYETAIAK" is absent in LP30K accessions from hemocytes showed loss of DNA sequences encoding the domain. The accessions H9J4F5, H9B440, A7LIK7 and H9B444 showed 92% identity with B. mori LP30K protein (NP_001095198.2) however the glucose binding domain I is absent in these accessions suggesting isoform- specific restricted fungal defense activity. Phylogeny tree of the LP30K homologues showed four groups including microvitellogenin and 30 kDa proteins showing functional diversity endorsed with evolutionary diversity. LP30K accessions with glucose binding domain diverged from that without glucose binding domain exemplify co-evolution for domain- dependent functional roles like storage and immune reactions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03685-x.

Small protein folds at the root of an ancient metabolic network

Life on Earth is driven by electron transfer reactions catalyzed by a suite of enzymes that comprise the superfamily of oxidoreductases (Enzyme Classification EC1). Most modern oxidoreductases are complex in their structure and chemistry and must have evolved from a small set of ancient folds. Ancient oxidoreductases from the Archean Eon between ca. 3.5 and 2.5 billion years ago have been long extinct, making it challenging to retrace evolution by sequence-based phylogeny or ancestral sequence reconstruction. However, three-dimensional topologies of proteins change more slowly than sequences. Using comparative structure and sequence profile-profile alignments, we quantify the similarity between proximal cofactor-binding folds and show that they are derived from a common ancestor. We discovered that two recurring folds were central to the origin of metabolism: ferredoxin and Rossmann-like folds. In turn, these two folds likely shared a common ancestor that, through duplication, recruitment, and diversification, evolved to facilitate electron transfer and catalysis at a very early stage in the origin of metabolism.

Nonparametric chemical descriptors for the calculation of ligand-biopolymer affinities with machine-learning scoring functions

The computational prediction of ligand-biopolymer affinities is a crucial endeavor in modern drug discovery and one that still poses major challenges. The choice of the appropriate computational method often reveals itself as a trade-off between accuracy and speed, with mathematical devices referred to as scoring functions being the fastest. Among the many shortcomings of scoring functions there is the lack of universal applicability to every molecular system. This is so largely due to their reliance on atom type perception and/or parametrization. This article proposes the use of nonparametric Model of Effective Radii of Atoms descriptors that can be readily computed for the entire Periodic Table and demonstrate that, in combination with machine learning algorithms, they can yield competitive performances and chemically meaningful insights.