Transmembrane Peptides as Sensors of the Membrane Physical State

Abstract

Cell membranes are commonly considered fundamental structures having multiple roles such as confinement, storage of lipids, sustain and control of membrane proteins. In spite of their importance, many aspects remain unclear. The number of lipid types is orders of magnitude larger than the number of amino acids, and this compositional complexity is not clearly embedded in any membrane model. A diffused hypothesis is that the large lipid palette permits to recruit and organize specific proteins controlling the formation of specialized lipid domains and the lateral pressure profile of the bilayer. Unfortunately, a satisfactory knowledge of lipid abundance remains utopian because of the technical difficulties in isolating definite membrane regions. More importantly, a theoretical framework where to fit the lipidomic data is still missing. In this work, we wish to utilize the amino acid sequence and frequency of the membrane proteins as bioinformatics sensors of cell bilayers. The use of an alignment-free method to find a correlation between the sequences of transmembrane portion of membrane proteins with the membrane physical state (MPS) suggested a new approach for the discovery of antimicrobial peptides.

Pseudo-semantic Approach to Study Model Membranes

“…It is possible to define an Expressed Features (EF) as a string of length l and a number of occurrence of the strings (o i ). The dictionary MEF contains all EFs in descending order starting from the sequences with larger o i [23].…”

Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology

“…[More details are available in Piotto et al. ( 2018 ).] The calculation of the distance matrix among 51 full proteomes is extremely fast and lasts few seconds on i3 processor.…”

Hydroxylated Fatty Acids: The Role of the Sphingomyelin Synthase and the Origin of Selectivity

“…However, the link between physical properties and cell signaling is complicated because of the many components and the characteristic dynamics of membranes [ 15 ]. Sphingolipids are central in determining the physical state of membranes and turn out to be bioactive molecules [ 16 ].…”