What stabilizes the 3_14-helix in beta^3-peptides? A conformational analysis using molecular simulation.

Beta-peptides are analogs of natural alpha-peptides and form a variety of remarkably stable structures. Having an additional carbon atom in the backbone of each residue, their folded conformation is not only influenced by the side-chain sequence but also and foremost by their substitution pattern. The precise mechanism by which the side chains interact with the backbone is, however, hitherto not completely known. In order to unravel the various effects by which the side chains influence the backbone conformation, we quantify to which extent the dihedral angles of a beta^3-substited peptide with an additional methyl group on the central C_alpha-atom can be regarded as independent degrees of freedom and analyze the distributions of these dihedral angles. We also selectively capture the steric effect of substituents on the C_alpha- and C_beta-atoms of the central residue by alchemically changing them into dummy atoms, which have no non-bonded interactions. We find that the folded state of the beta^3-peptide is primarily stabilized by a steric exclusion of large parts of the unfolded state (entropic effect) and only subsequently by mutual dependence of the psi-dihedral angles (enthalpic effect). The folded state of beta-peptides is stabilized by a different mechanism than that of alpha-peptides

What stabilizes the 3_14-helix in beta^3-peptides? A conformational analysis using molecular simulation.

Beta-peptides are analogs of natural alpha-peptides and form a variety of remarkably stable structures. Having an additional carbon atom in the backbone of each residue, their folded conformation is not only influenced by the side-chain sequence but also and foremost by their substitution pattern. The precise mechanism by which the side chains interact with the backbone is, however, hitherto not completely known. In order to unravel the various effects by which the side chains influence the backbone conformation, we quantify to which extent the dihedral angles of a beta^3-substited peptide with an additional methyl group on the central C_alpha-atom can be regarded as independent degrees of freedom and analyze the distributions of these dihedral angles. We also selectively capture the steric effect of substituents on the C_alpha- and C_beta-atoms of the central residue by alchemically changing them into dummy atoms, which have no non-bonded interactions. We find that the folded state of the beta^3-peptide is primarily stabilized by a steric exclusion of large parts of the unfolded state (entropic effect) and only subsequently by mutual dependence of the psi-dihedral angles (enthalpic effect). The folded state of beta-peptides is stabilized by a different mechanism than that of alpha-peptides

A combined solid-state NMR and MD characterization of the stability and dynamics of the HET-s(218-289) prion in its amyloid conformation.

The three-dimensional structure of amyloid fibrils of the prion-forming part of the HET-s protein [HET-s(218-289)], as determined by solid-state NMR, contains rigid and remarkably well-ordered parts, as witnessed by the narrow solid-state NMR line widths for this system. On the other hand, high-resolution magic-angle-spinning (HRMAS) NMR results have shown that HET-s(218-289) amyloid fibrils contain highly flexible parts as well. Here, we further explore this unexpected behaviour using solid-state NMR and molecular dynamics (MD). The NMR data provide new information on order and dynamics in the rigid and flexible parts of HET-s(218-289), respectively. The MD study addresses whether or not small multimers, in an amyloid conformation, are stable on the 10 ns timescale of the MD run and provides insight into the dynamic parameters on the nanosecond timescale. The atom-positional, root-mean-squared fluctuations (RMSFs) and order parameters S-2 obtained are in agreement with the NMR data. A flexible loop and the N terminus exhibit dynamics on the ps-ns timescale, whereas the hydrophobic core of HET-s(218-289) is rigid. The high degree of order in the core region of HET-s(218-289) amyloids, as observed in the MID simulations, is in agreement with the narrow, solid-state, NMR lines. Finally, we employed MD to predict the behaviour of the salt-bridge network in HET-s(218289), which cannot be obtained easily by experiment. Simulations at different temperatures indicated that the network is highly dynamic and that it contributes to the thermostability of the HET-s(218-289) amyloids

Solid-state NMR, electrophysiology and molecular dynamics characterization of human VDAC2.

The voltage-dependent anion channel (VDAC) is the most abundant protein of the outer mitochondrial membrane and constitutes the major pathway for the transport of ADP, ATP, and other metabolites. In this multidisciplinary study we combined solid-state NMR, electrophysiology, and molecular dynamics simulations, to study the structure of the human VDAC isoform 2 in a lipid bilayer environment. We find that the structure of hVDAC2 is similar to the structure of hVDAC1, in line with recent investigations on zfVDAC2. However, hVDAC2 appears to exhibit an increased conformational heterogeneity compared to hVDAC1 which is reflected in broader solid-state NMR spectra and less defined electrophysiological profiles

NMR-Based Detection of Hydrogen/Deuterium Exchange in Liposome-Embedded Membrane Proteins.

Membrane proteins play key roles in biology. Determination of their structure in a membrane environment, however, is highly challenging. To address this challenge, we developed an approach that couples hydrogen/deuterium exchange of membrane proteins to rapid unfolding and detection by solution-state NMR spectroscopy. We show that the method allows analysis of the solvent protection of single residues in liposome-embedded proteins such as the 349-residue Tom40, the major protein translocation pore in the outer mitochondrial membrane, which has resisted structural analysis for many years.peerReviewe