PVPred-SCM: Improved Prediction and Analysis of Phage Virion Proteins Using a Scoring Card Method

Although, existing methods have been successful in predicting phage (or bacteriophage) virion proteins (PVPs) using various types of protein features and complex classifiers, such as support vector machine and naïve Bayes, these two methods do not allow interpretability. However, the characterization and analysis of PVPs might be of great significance to understanding the molecular mechanisms of bacteriophage genetics and the development of antibacterial drugs. Hence, we herein proposed a novel method (PVPred-SCM) based on the scoring card method (SCM) in conjunction with dipeptide composition to identify and characterize PVPs. In PVPred-SCM, the propensity scores of 400 dipeptides were calculated using the statistical discrimination approach. Rigorous independent validation test showed that PVPred-SCM utilizing only dipeptide composition yielded an accuracy of 77.56%, indicating that PVPred-SCM performed well relative to the state-of-the-art method utilizing a number of protein features. Furthermore, the propensity scores of dipeptides were used to provide insights into the biochemical and biophysical properties of PVPs. Upon comparison, it was found that PVPred-SCM was superior to the existing methods considering its simplicity, interpretability, and implementation. Finally, in an effort to facilitate high-throughput prediction of PVPs, we provided a user-friendly web-server for identifying the likelihood of whether or not these sequences are PVPs. It is anticipated that PVPred-SCM will become a useful tool or at least a complementary existing method for predicting and analyzing PVPs

Structural and transport phenomena of urocanate-based proton carrier in sulfonated poly(ether ether ketone) membrane composite

Proton transport is one of crucial phenomena in electrolytic part highly considered to overcome a limit in fuel cell efficiency improvement. Proton conducting organic electrolyte was modeled and simulated at atomistic level of calculation by doping of butyl urocanate (C4U), a composite material with imidazole substructure, with sulfonated poly(ether ether ketone) (SPEEK) amorphous membrane at various working temperature. Molecular dynamics simulations were used to investigate structural and dynamics characteristic of C4U in the membrane comparing with the SPEEK-hydronium membrane model as a control. From simulations, thermal effect on water and proton carriers cluster surrounding the sulfonate groups was explored. At higher temperature, the more transport dynamics of C4U ions in SPEEK membranes were found than that of hydronium ions in the control system. Likewise, phase separation of hydrophobic and hydrophilic parts was taken into consideration here. A critical role of the enhancing proton conductivity by increasing the diffusion coefficient at temperature beyond C4U melting point in composite polymer membrane was emphasized