TMPfold: A Web Tool for Predicting Stability of Transmembrane α-Helix Association

BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins

“…Experimental data about the association energy of a series of 16 membrane structures that contain a single α -helix crossing the membrane were collected from Lomize et al (2020) . We analyzed how the MPr score of these transmembrane structures change upon dimerization or tetramerization and whether there is a quantitative relation between this score and the experimental values.…”

A single residue deletion in the barley HKT1;5 P189 variant restores plasma membrane localisation but not Na+ conductance

“…Our observations suggest several possibilities: (i) α-helix 6 (carrying P189) cannot form stable intra-helical contacts and/or folds transiently after it emerges from a ribosome; (ii) α-helix 6 does not fold fast enough thus exposes proteolytic sites; (iii) αhelix 6 cannot form an α-hairpin -α-helical folding pairwith a neighbouring α-helix. These αhairpins play crucial roles as the folding of nuclei in polytopic membrane proteins needs to be completed [46,48]. We postulate that one or a combination of (i-iii) could prevent P189 from passing intracellular control mechanisms, therefore preventing routing to the plasma membrane.…”

“…In prokaryotes, polytopic membrane protein insertions J o u r n a l P r e -p r o o f happen mainly co-translationally [51], while in eukaryotes this occurs at an endoplasmic reticulum via elaborate pathways involving membrane protein insertase complexes [53], or via spontaneous insertion of nascent chains and translocon-unassisted folding [54]. Novel biocomputational approaches, such as TMPfold [46], are needed to evaluate the protein folding pathways of membrane proteins. Here, we used this approach together with 3D protein modelling and MD simulations to predict transmembrane α-helical assembly pathways of HvHKT1;5 proteins and their M372del mutants.…”

“…Calculations of energies in pairwise structurally associated α-helical regions and protein folding pathways of polytopic L189 and P189 models, and L189 M372del and P189 M372del mutants were performed in TMPfold [46]. Compared to our earlier work [8], where the topology of HvHKT1;5 taken from PolyPhobius [47], in this work we extended the number of α-helices defined by the Database of Secondary Structure (DSS) algorithm implemented in PYMOL (DSS defines secondary structures based on the backbone geometry and hydrogen bonding patterns) and excluded those that were equal or less than three residues in length.…”

“…We used TMPfold [46] to predict tentative transmembrane α-helical association or folding pathway parameters in HvHKT1;5 variants and their M372del mutant proteins, where the folding pathways or equations are calculated based on: (i) transmembrane α-helices are inserted into a membrane sequentially; (ii) each α-helix is added in a separate step; (iii) newly synthesised αhelix associates stably with a previous α-helix or a nucleus (defined as an assembly of sequentially adjacent α-helices); and (iv) sequentially adjacent structures associate first.…”