Secondary Structures of Proteins: A Comparison of Models and Experimental Results

Predicting the Assembly of the Transmembrane Domains of Viral Channel Forming Proteins and Peptide Drug Screening Using a Docking Approach

A de novo assembly algorithm is provided to propose the assembly of bitopic transmembrane domains (TMDs) of membrane proteins. The algorithm is probed using, in particular, viral channel forming proteins (VCPs) such as M2 of influenza A virus, E protein of severe acute respiratory syndrome corona virus (SARS-CoV), 6K of Chikungunya virus (CHIKV), SH of human respiratory syncytial virus (hRSV), and Vpu of human immunodeficiency virus type 2 (HIV-2). The generation of the structures is based on screening a 7-dimensional space. Assembly of the TMDs can be achieved either by simultaneously docking the individual TMDs or via a sequential docking. Scoring based on estimated binding energies (EBEs) of the oligomeric structures is obtained by the tilt to decipher the handedness of the bundles. The bundles match especially well for all-atom models of M2 referring to an experimentally reported tetrameric bundle. Docking of helical poly-peptides to experimental structures of M2 and E protein identifies improving EBEs for positively charged (K,R,H) and aromatic amino acids (F,Y,W). Data are improved when using polypeptides for which the coordinates of the amino acids are adapted to the Cα coordinates of the respective experimentally derived structures of the TMDs of the target proteins.

Wide-Line NMR Melting Diagrams, Their Thermodynamic Interpretation, and Secondary Structure Predictions for A30P and E46K α-Synuclein

Parkinson's disease is thought to be caused by aggregation of the intrinsically disordered protein, α-synuclein. Two amyloidogenic variants, A30P, and E46K familial mutants were investigated by wide-line ¹H NMR spectrometry as a completion of our earlier work on wild-type and A53T α-synuclein (Bokor M. et al. WT and A53T α-synuclein systems: melting diagram and its new interpretation. Int. J. Mol. Sci.2020, 21, 3997.). A monolayer of mobile water molecules hydrates A30P α-synuclein at the lowest potential barriers (temperatures), while E46K α-synuclein has here third as much mobile hydration, insufficient for functionality. According to wide-line ¹H NMR results and secondary structure predictions, E46K α-synuclein is more compact than the A30P variant and they are more compact than the wild type (WT) and A53T variants. Linear hydration vs potential barrier sections of A30P α-synuclein shows one and E46K shows two slopes. The different slopes of the latter between potential barriers E _a,1 and E _a,2 reflect a change in water-protein interactions. The 31-32% homogeneous potential barrier distribution of the protein-water bonds refers to a non-negligible amount of secondary structures in all four α-synuclein variants. The secondary structures detected by wide-line ¹H NMR are solvent-exposed α-helices, which are predicted by secondary structure models. β-sheets are only minor components of the protein structures as three- and eight-state predicted secondary structures are dominated by α-helices and coils.