ANGT_HUMAN[448–462], an Anorexigenic Peptide Identified using Plasma Peptidomics

Integrating a Multi-label Deep Learning Approach with Protein Information to Compare Bioactive Peptides in Brain and Plasma

Peptide therapeutics is gaining momentum. Advances in the field of peptidomics have enabled researchers to harvest vital information from various organisms and tissue types concerning peptide existence, expression and function. The development of mass spectrometry techniques for high-throughput peptide quantitation has paved the way for the identification and discovery of numerous known and novel peptides. Though much has been achieved, scientists are still facing difficulties when it comes to reducing the search space of the large mass spectrometry-generated peptidomics datasets and focusing on the subset of functionally relevant peptides. Moreover, there is currently no straightforward way to analytically compare the distributions of bioactive peptides in distinct biological samples, which may reveal much useful information when seeking to characterize tissue- or fluid-specific peptidomes. In this chapter, we demonstrate how to identify, rank, and compare predicted bioactive peptides and bioactivity distributions from extensive peptidomics datasets. To aid this task, we utilize MultiPep, a multi-label deep learning approach designed for classifying peptide bioactivities, to identify bioactive peptides. The predicted bioactivities are synergistically combined with protein information from the UniProt database, which assist in navigating through the jungle of putative therapeutic peptides and relevant peptide leads.

Modulation of the H+/ATP coupling ratio by ADP and ATP as a possible regulatory feature in the F-type ATP synthases

F-type ATP synthases are transmembrane enzymes, which play a central role in the metabolism of all aerobic and photosynthetic cells and organisms, being the major source of their ATP synthesis. Catalysis occurs via a rotary mechanism, in which the free energy of a transmembrane electrochemical ion gradient is converted into the free energy of ATP phosphorylation from ADP and Pi, and vice versa. An ADP, tightly bound to one of the three catalytic sites on the stator head, is associated with catalysis inhibition, which is relieved by the transmembrane proton gradient and by ATP. By preventing wasteful ATP hydrolysis in times of low osmotic energy and low ATP/ADP ratio, such inhibition constitutes a classical regulatory feedback effect, likely to be an integral component of in vivo regulation. The present miniview focuses on an additional putative regulatory phenomenon, which has drawn so far little attention, consisting in a substrate-induced tuning of the H+/ATP coupling ratio during catalysis, which might represent an additional key to energy homeostasis in the cell. Experimental pieces of evidence in support of such a phenomenon are reviewed.