All-atom structure of F-BAR domain lattice on the formed membrane tube.

<p>(Left) Coarse-grained tube structure from simulation TUBULATION, as depicted in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002892#pcbi-1002892-g006" target="_blank">Fig. 6</a>. (Right) All-atom structure constructed from the SBCG structure. (Insert right) Close up view of all-atom structure, rendered in so-called cartoon representation. Residues Lys66, Arg47 are shown in van der Waals representation and colored in red; Glu285, Asp161 are represented in the same way, but colored in blue.</p

Fibril Elongation by Aβ_17–42: Kinetic Network Analysis of Hybrid-Resolution Molecular Dynamics Simulations

A critical step of β-amyloid fibril formation is fibril elongation in which amyloid-β monomers undergo structural transitions to fibrillar structures upon their binding to fibril tips. The atomic detail of the structural transitions remains poorly understood. Computational characterization of the structural transitions is limited so far to short Aβ segments (5–10 aa) owing to the long time scale of Aβ fibril elongation. To overcome the computational time scale limit, we combined a hybrid-resolution model with umbrella sampling and replica exchange molecular dynamics and performed altogether ∼1.3 ms of molecular dynamics simulations of fibril elongation for Aβ_17–42. Kinetic network analysis of biased simulations resulted in a kinetic model that encompasses all Aβ segments essential for fibril formation. The model not only reproduces key properties of fibril elongation measured in experiments, including Aβ binding affinity, activation enthalpy of Aβ structural transitions and a large time scale gap (τ_lock/τ_dock = 10³–10⁴) between Aβ binding and its structural transitions, but also reveals detailed pathways involving structural transitions not seen before, namely, fibril formation both in hydrophobic regions L17-A21 and G37-A42 preceding fibril formation in hydrophilic region E22-A30. Moreover, the model identifies as important kinetic intermediates strand–loop–strand (SLS) structures of Aβ monomers, long suspected to be related to fibril elongation. The kinetic model suggests further that fibril elongation arises faster at the fibril tip with exposed L17-A21, rather than at the other tip, explaining thereby unidirectional fibril growth observed previously in experiments

Interaction of an individual F-BAR domain with a lipid membrane.

<p>(A) Lipid membrane interaction with the wild type F-BAR (WT) domain (as described in simulation WT1) and F-BAR domain with positive charges on residues along the inner leaflet abolished (as described in Methods for simulation NC). WT binds to the membrane in 30 ns and generates a 28 nm radius of curvature within 100 ns. In the case of NC, the F-BAR domain does not bind to the membrane over 80 ns and the membrane remains flat. Membrane lipids are colored in grey; F-BAR proteins are colored in blue and orange to distinguish the monomers. (B) Locations of residues 56 to 60 and the positively-charged residues along the inner surface of the F-BAR dimer. Location of residues 56 to 60 at time (insert left) and (insert right); the membrane is shown in grey surface representation; F-BAR proteins are colored in blue and orange to distinguish the monomers. Representative residues interacting with lipid are colored in green, brown, blue, purple and grey as well as highlighted by red arrows; interacting lipids are shown in green stick representation. (C) Number of contacts formed between negatively-charged DOPS lipid headgroups and positively charged residues along the inner surface of F-BAR domains. A contact is considered formed if nitrogen atoms of Arg/Lys residues are within 5<i>A?</i> of an oxygen atom of a DOPS lipid headgroup. Contact of representative residues with lipid are colored in green, brown, blue, purple and grey as in (B). Additional contacting residues are shown in Fig. S1 in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002892#pcbi.1002892.s001" target="_blank">Text S1</a>.</p

Membrane tubules induced by F-BAR domain lattice.

<p>(A) Membrane tubule formed by edge-to-edge fusion. As explained in the text, the end result of simulation TUBULATION, shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002892#pcbi-1002892-g006" target="_blank">Figure 6b</a>, had its free edges forcibly fused, the resulting membrane tubule being presented here. The membrane tubule is shown from side and top; in the latter case the F-BAR domains have been removed, leaving solely the lipids, depicted in green; individual F-BAR domains are differentiated by color. Shown is also the membrane tubule structure after simulation with F-BAR domain removed, quite clearly the tubule structure remained intact. (B) Membrane tubules formed as in (A), but by edge-to-edge fusion forming a T-junction. The membrane tubule is shown from side and top; in the latter case the F-BAR domains have been removed, leaving solely the lipid. Shown is also the membrane tubule structure after simulation with F-BAR domain removed. Colors are the same as in (A).</p

Mechanism of Substrate Translocation by a Ring-Shaped ATPase Motor at Millisecond Resolution

Ring-shaped, hexameric ATPase motors fulfill key functions in cellular processes, such as genome replication, transcription, or protein degradation, by translocating a long substrate through their central pore powered by ATP hydrolysis. Despite intense research efforts, the atomic-level mechanism transmitting chemical energy from hydrolysis into mechanical force that translocates the substrate is still unclear. Here we employ all-atom molecular dynamics simulations combined with advanced path sampling techniques and milestoning analysis to characterize how mRNA substrate is translocated by an exemplary homohexameric motor, the transcription termination factor Rho. We find that the release of hydrolysis product (ADP + Pi) triggers the force-generating process of Rho through a 0.1 millisecond-long conformational transition, the time scale seen also in experiment. The calculated free energy profiles and kinetics show that Rho unidirectionally translocates the single-stranded RNA substrate via a population shift of the conformational states of Rho; upon hydrolysis product release, the most favorable conformation shifts from the pretranslocation state to the post-translocation state. Via two previously unidentified intermediate states, the RNA chain is seen to be pulled by six K326 side chains, whose motions are induced by highly coordinated relative translation and rotation of Rho’s six subunits. The present study not only reveals in new detail the mechanism employed by ring-shaped ATPase motors, for example the use of loosely bound and tightly bound hydrolysis reactant and product states to coordinate motor action, but also provides an effective approach to identify allosteric sites of multimeric enzymes in general

Membrane curvature induced by lattices of F-BAR domains.

<p>(A) Dependence of membrane curvature on F-BAR domain density. Shown is curvature generated by lattices with F-BAR dimer densities of 5, 8, 10, 13 and 15 dimers per . A density of 10 dimers per generates the highest curvature, with radius of curvature . (B) Membrane curvature induced by F-BAR domains forming lattices of different angle . An angle of produces the highest curvature, with radius of curvature . (C) Dependence of membrane curvature on inter-dimer distance. A distance of 21.5 nm produces the highest curvature, with radius of curvature R = 33 nm. (D) Dependence of membrane curvature on staggered or aligned arrangement of F-BAR domains. A staggered arrangement produces higher curvature than an aligned arrangement. F-BAR domains and lipid membranes shown on the left of (A–D) are shown in color and in grey, respectively; individual F-BAR domains are differentiated by color.</p

All-atom and SBCG model of F-BAR domain and membrane.

<p>The F-BAR domain is shown as the all-atom (A) and the SBCG (B) model in side-view and top-view, with monomers differentiated by colors purple and orange. Charge distribution of all-atom (C) and SBCG (D) F-BAR domain. In the all-atom model, positively and negatively charged residues are shown in red and blue, respectively. In the SBCG model, the charge on each bead is color-coded on a scale from (blue) to (red). All-atom (E) and SBCG (F) model of the DOPC/DOPS membrane. The neutral DOPC head groups are colored blue, and the negatively charged head groups on DOPS are colored in red. Starting (top) and final (bottom) conformation of all-atom (G) and SBCG (H) model of a single F-BAR domain and membrane.</p

Conformation of F-BAR domain lattices looking up from the membrane towards the protein.

<p>Individual F-BAR domains are differentiated by color. Initial (A) and final (B) conformation of the F-BAR domain lattices on top of the membrane taken from one of the systems, simulations LATTICES, shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002892#pcbi-1002892-g004" target="_blank">Fig. 4</a>; the density is 13 dimers per . Positions where the concave surface of the F-BAR domains is blocked by neighboring F-BAR domain tips are marked by orange arrows. (C) Parts of F-BAR domain lattices at different densities.</p

Conformational change of F-BAR domain during interaction with the membrane.

<p>Change of membrane curvature and of angles during simulations WT1, WT2, NC, NL1 and NL2 (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002892#pcbi-1002892-t001" target="_blank">Table 1</a>). Original data are shown in gray and running averages over 10 ns in color. Conformations of the F-BAR domain and interaction with the membrane are shown at 0, 40, 80 and 120 ns for simulation WT1. Helices 2 to 4 are colored blue, purple and green, respectively; tails of membrane lipids are colored grey; the neutral DOPC head groups are colored blue and the negatively charged DOPS head groups red.</p

Characterization of Folding Mechanisms of Trp-Cage and WW-Domain by Network Analysis of Simulations with a Hybrid-Resolution Model

In this study, we apply a hybrid-resolution model, namely, PACE, to characterize the free energy surfaces (FESs) of Trp-cage and a WW-domain variant along with the respective folding mechanisms. Unbiased, independent simulations with PACE are found to achieve together multiple folding and unfolding events for both proteins, allowing us to perform network analysis of the FESs to identify folding pathways. PACE reproduces for both proteins expected complexity hidden in the folding FESs, in particular metastable non-native intermediates. Pathway analysis shows that some of these intermediates are, actually, on-pathway folding intermediates and that intermediates kinetically closest to the native states can be either critical on-pathway or off-pathway intermediates, depending on the protein. Apart from general insights into folding, specific folding mechanisms of the proteins are resolved. We find that Trp-cage folds via a dominant pathway in which hydrophobic collapse occurs before the N-terminal helix forms; full incorporation of Trp6 into the hydrophobic core takes place as the last step of folding, which, however, may not be the rate-limiting step. For the WW-domain variant studied, we observe two main folding pathways with opposite orders of formation of the two hairpins involved in the structure; for either pathway, formation of hairpin 1 is more likely to be the rate-limiting step. Altogether, our results suggest that PACE combined with network analysis is a computationally efficient and valuable tool for the study of protein folding