Structure and dynamics of two β-peptides in solution from molecular dynamics simulations validated against experiment

We have studied two different β-peptides in methanol using explicit solvent molecular dynamics simulations and the GROMOS 53A6 force field: a heptapeptide (peptide 1) expected to form a left-handed 314-helix, and a hexapeptide (peptide 2) expected to form a β-hairpin in solution. Our analysis has focused on identifying and analyzing the stability of the dominant secondary structure conformations adopted by the peptides, as well as on comparing the experimental NOE distance upper bounds and 3J-coupling values with their counterparts calculated on the basis of the simulated ensembles. Moreover, we have critically compared the present results with the analogous results obtained with the GROMOS 45A3 (peptide 1) and 43A1 (peptide 2) force fields. We conclude that within the limits of conformational sampling employed here, the GROMOS 53A6 force field satisfactorily reproduces experimental findings regarding the behavior of short β-peptides, with accuracy that is comparable to but not exceeding that of the previous versions of the force field. GCE legend Conformational clustering analysis of the simulated ensemble of a ß-hexapeptide with two different simulation setups (a and b). The central members of all of the clusters populating more than 5% of all of the structures are shown, together with the most dominant hydrogen bonds and the corresponding percentages of cluster members containing the

Structure and dynamics of two β-peptides in solution from molecular dynamics simulations validated against experiment

ISSN:0175-7571ISSN:1432-101

Solid-state NMR 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 plasticity compared to hVDAC1 which is reflected in broader solid-state NMR spectra and less defined electrophysiological profiles

Structural characterization of liposome-embedded ncTom40 by H/D exchange coupled to solution-state NMR.

<p>(a) Enlarged spectral regions of [¹H, ¹⁵N]-HSQC spectra at increasing back-exchange times. To reduce signal overlap, ncTom40 was selectively ¹⁵N-labeled at ALA, HIS, ILE, MET, THR. Time points indicate the time after start of the first HSQC. The dissolution buffer contained 75% D₂O. Sequence-specific resonance assignments are indicated. (b) Sequence-specific signal intensities in the first HSQC after dissolution in 100% D₂O buffer. (c) NMR signal intensity change of residues in panel (a) during back-exchange in 75% D₂O. Intensity values were normalized on the basis of the noise level in the spectra. Error bars are based on signal-to-noise. (d) Protonation ratios for residues of Tom40 at the beginning of back exchange. (e) Protonation ratios shown in (d) were mapped onto the topology model of ncTom40, which was predicted on the basis of its homology to hVDAC1. Residues predicted to be in a β-strand or α-helix are boxed. Green-shaded (red-shaded) residues have protonation ratios larger (lower) than 0.3. Residues shown in white were not analyzed due to signal overlap, low signal-to-noise or missing resonance assignment.</p

Recombinant ncTom40 has a β-barrel structure. (a) Far UV CD spectra of ncTom40 in decylmaltoside. (b) Superposition of ¹³C-¹³C proton driven spin diffusion spectra of ncTom40 (red) and hVDAC1 (green; reproduced from [4]), both in DMPC liposomes. The mixing time was 15 ms.

<p>Recombinant ncTom40 has a β-barrel structure. (a) Far UV CD spectra of ncTom40 in decylmaltoside. (b) Superposition of ¹³C-¹³C proton driven spin diffusion spectra of ncTom40 (red) and hVDAC1 (green; reproduced from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112374#pone.0112374-Schneider1" target="_blank">[4]</a>), both in DMPC liposomes. The mixing time was 15 ms.</p

Atomic models of de novo designed cc beta-met amyloid-like fibrils

The common characteristics of amyloid and amyloid-like fibrils from disease- and non-disease-associated proteins offer the prospect that well-defined model systems can be used to systematically dissect the driving forces of amyloid formation. We recently reported the de novo designed cc peptide model system that forms a native-like coiled-coil structure at low temperatures and which can be switched to amyloid-like fibrils by increasing the temperature. Here, we report a detailed molecular description of the system in its fibrillar state by characterizing the cc beta-Met variant using several microscopic techniques, circular dichroism spectroscopy, X-ray fiber diffraction, solid-state nuclear magnetic resonance, and molecular dynamics calculations. We show that cc beta-Met forms amyloid-like fibrils of different morphologies on both the macroscopic and atomic levels, which can be controlled by variations of assembly conditions. Interestingly, heterogeneity is also observed along single fibrils. We propose atomic models of the cc beta-Met amyloid-like fibril, which are in good agreement with all experimental data. The models provide a rational, explanation why oxidation of methionine residues completely abolishes cc beta-Met amyloid fibril formation, indicating that a small number of site-specific hydrophobic interactions can play a major role in the packing of polypeptide-chain segments within amyloid fibrils. The detailed structural information available for the cc beta model system provides a strong molecular basis for understanding the influence and relative contribution of hydrophobic interactions on native-state stability, kinetics of fibril formation, fibril packing, and polymorphism. (C) 2007 Elsevier Ltd. All rights reserved

Scheme illustrating the H/D exchange strategy developed for membrane proteins (blue) reconstituted into liposomes (yellow).

<p>A white color indicates H₂O buffer, black color 100% D₂O buffer and grey color the dissolution buffer, which contains 4 M GdnSCN. During the incubation period in 100% D₂O solvent exposed residues will exchange amide protons against deuterium (lower row, middle panel). They will therefore not be visible in the denatured monomer (lower right panel).</p

APSY experiments recorded at different temperatures and assignments obtained for denatured ncTom40 (339 non-proline residues) by MARS [31].

<p>Assignments classified by MARS as low are not reliable and were excluded from further analysis.</p><p>APSY experiments recorded at different temperatures and assignments obtained for denatured ncTom40 (339 non-proline residues) by MARS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112374#pone.0112374-Panchal1" target="_blank">[31]</a>.</p