Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations

<div><p>Cytoplasmic dynein is a giant ATP-driven molecular motor that proceeds to the minus end of the microtubule (MT). Dynein hydrolyzes ATP in a ring-like structure, containing 6 AAA+ (ATPases associated with diverse cellular activities) modules, which is ~15 nm away from the MT binding domain (MTBD). This architecture implies that long-distance allosteric couplings exist between the AAA+ ring and the MTBD in order for dynein to move on the MT, although little is known about the mechanisms involved. Here, we have performed comprehensive molecular simulations of the dynein motor domain based on pre- and post- power-stroke structural information and in doing so we address the allosteric conformational changes that occur during the power-stroke and recovery-stroke processes. In the power-stroke process, the N-terminal linker movement was the prerequisite to the nucleotide-dependent AAA1 transition, from which a transition cascade propagated, on average, in a circular manner on the AAA+ ring until it reached the AAA6/C-terminal module. The recovery-stroke process was initiated by the transition of the AAA6/C-terminal, from which the transition cascade split into the two directions of the AAA+ ring, occurring both clockwise and anti-clockwise. In both processes, the MTBD conformational change was regulated by the AAA4 module and the AAA5/Strut module.</p></div

Analysis of the recovery-stroke process.

<p>(A) A representative trajectory for the AAA6↓ simulation. (B) Local structural change at the interface between AAA6/C-terminal module and the AAA1 in the standard setup simulation. The post-power-stroke structure (left) and an intermediate snapshot structure (right) are depicted. For the latter, the atomic structure was reconstituted from a coarse-grained snapshot. E4297 in the AAA6/C-terminal module and R2084 in the AAA1 module interact in the post-power-stroke structure, whereas they are apart in the intermediate structure. Atomistic model was reconstructed by the protocol given in Method. (C) Local structural change at the interface between the AAA6/C-terminal module (red for the post-power-stroke structure), salmon pink (100 x 10⁴ MD step), and white (103 x 10⁴ MD step)) and the AAA5 module (orange for the post-power-stroke structure), light orange (100 x 10⁴ MD step), and white (103 x 10⁴ MD step) in the standard setup simulation. Arrows labeled with 1 and 2 represent the sequential movement. (D) Three examples of the conformational change in MTBD/Stalk along scaled time. (E) Averaged conformational change in the MTBD/Stalk along scaled time for the forward (red) and recovery (blue) strokes. The time in each trajectory is scaled to be zero at the time of the AAA4 (AAA5) transitions and one at the time of the AAA5 (AAA4) transitions for the forward (recovery) strokes.</p

Template Induced Conformational Change of Amyloid-β Monomer

Population of aggregation-prone conformers for the monomeric amyloid-β (Aβ) can dramatically speed up its fibrillar aggregation. In this work, we study the effect of preformed template on the conformational distributions of the monomeric Aβ by replica exchange molecular dynamics. Our results show that the template consisting of Aβ peptides with cross-β structure can induce the formation of β-rich conformations for the monomeric Aβ, which is the key feature of the aggregation-prone conformers. Similar effect is observed when the hIAPP peptides and poly alanine peptides were used as templates, suggesting that the template effect is insensitive to the sequence details of the template peptides. In comparison, the template with helical structure has no significant effects on the β-propensity of the monomeric Aβ. Analysis to the interaction details revealed that the template tends to disrupt the intrapeptide interactions of the monomeric Aβ, which are absent in the fibrillar state, suggesting that the preformed template can reorganize the intrapeptide interactions of the monomeric Aβ during the capturing stage and reduce the energy frustrations for the fibrillar aggregations

Recovery-stroke simulations in the standard setup.

<p>(A) A representative trajectory of the reaction coordinates χ for the eight modules along the MD step. (B) The order map. (C) The pair-rate map. (D) The sorted order map. Refer to the caption for <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005748#pcbi.1005748.g002" target="_blank">Fig 2</a> for more information.</p

Analysis of the power-stroke process.

<p>(A) A representative trajectory for the AAA1↑ simulation. (B) Local structural change at the interface between the linker and AAA1 in the standard setup simulation. The middle and the right structures represent the pre-power-stroke and an intermediate snapshot structure, respectively. The left-hand cartoon indicates the position of the structure within the entire motor domain. Important interactions are indicated by dashed lines. Atomistic model was reconstructed by the protocol given in Method. (C) Three examples of the conformational change in MTBD/Stalk along scaled time. (D) Average conformational change in MTBD/Stalk along scaled time for power-strokes. The time in each trajectory is scaled.</p

Localized Frustration and Binding-Induced Conformational Change in Recognition of 5S RNA by TFIIIA Zinc Finger

Protein TFIIIA is composed of nine tandemly arranged Cys₂His₂ zinc fingers. It can bind either to the 5S RNA gene as a transcription factor or to the 5S RNA transcript as a chaperone. Although structural and biochemical data provided valuable information on the recognition between the TFIIIIA and the 5S DNA/RNA, the involved conformational motions and energetic factors contributing to the binding affinity and specificity remain unclear. In this work, we conducted MD simulations and MM/GBSA calculations to investigate the binding-induced conformational changes in the recognition of the 5S RNA by the central three zinc fingers of TFIIIA and the energetic factors that influence the binding affinity and specificity at an atomistic level. Our results revealed drastic interdomain conformational changes between these three zinc fingers, involving the exposure/burial of several crucial DNA/RNA binding residues, which can be related to the competition between DNA and RNA for the binding of TFIIIA. We also showed that the specific recognition between finger 4/finger 6 and the 5S RNA introduces frustrations to the nonspecific interactions between finger 5 and the 5S RNA, which may be important to achieve optimal binding affinity and specificity

The power-stroke simulations in the standard setup.

<p>(A) A representative trajectory of the reaction coordinates χ for the eight modules along the MD step. (B) The order map. Each square represents the probability that the transition in the region in the horizontal axis occurred before that in the region in the vertical axis over 30 trajectories. (C) The pair rate map representing <i>k</i>(b|a). (D) The sorted order map. The data in (B) is rearranged so that the summation in each column is in descending order. The same color code is used as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005748#pcbi.1005748.g001" target="_blank">Fig 1</a>.</p

Structure of dynein motor domain.

<p>(A) Structure models for the pre-power-stroke structure (left, modeled from 4RH7, the protein data bank id) and the post-power-stroke structure (modeled from 3VKH and 3J1T). (B) Cartoon view of the two structures with the definition of the eight multiple-basin systems. A unified color code is used to distinguish the eight modules throughout this paper; from N-terminus, the linker is in purple, the AAA1 is in blue, the AAA2 is in cyan, the AAA3 is in green, the AAA4 is in yellow, the MTBD/Stalk is in grey, the AAA5 is in orange, and the AAA6/C-terminal modules is in red.</p

The Balanced Insulating Performance and Mechanical Property of PP by Introducing PP‑<i>g</i>‑PS Graft Copolymer and SEBS Elastomer

The PP/PP-<i>g</i>-PS/SEBS blends are prepared by melt extrusion in order to improve both insulating properties and toughness of PP. SEBS is used to reduce the rigidity of PP, while the insulating properties are improved by adding PP-<i>g</i>-PS without decreasing mechanical properties. The microstructure of PP blends is carefully investigated by SEM, DMA, XRD, and DSC. It is interesting to find that a core–shell dispersion phase formed in the blend with the adding of PP-<i>g</i>-PS, and the size of core is decreased while the thickness of shell is increased with further increasing volume of PP-<i>g</i>-PS. Due to this special structure, the nucleation ability of SEBS is decreased. Meanwhile, the rigid segments and compatibilization effect of PP-<i>g</i>-PS not only increased the glass transition temperature of both PP and SEBS, but also enhanced their adhesion. Therefore, the electrical properties were increased without decreasing the mechanical properties of the blends. Consequently, an insulation material with excellent mechanical properties was obtained

Structure Prediction of RNA Loops with a Probabilistic Approach

<div><p>The knowledge of the tertiary structure of RNA loops is important for understanding their functions. In this work we develop an efficient approach named RNApps, specifically designed for predicting the tertiary structure of RNA loops, including hairpin loops, internal loops, and multi-way junction loops. It includes a probabilistic coarse-grained RNA model, an all-atom statistical energy function, a sequential Monte Carlo growth algorithm, and a simulated annealing procedure. The approach is tested with a dataset including nine RNA loops, a 23S ribosomal RNA, and a large dataset containing 876 RNAs. The performance is evaluated and compared with a homology modeling based predictor and an <i>ab initio</i> predictor. It is found that RNApps has comparable performance with the former one and outdoes the latter in terms of structure predictions. The approach holds great promise for accurate and efficient RNA tertiary structure prediction.</p></div