Effect of a cis-4-Aminopiperidine-3-carboxylic Acid (cis-APiC) Residue on Mixed-helical Folding of Unnatural Peptides

The α/β-peptide 11/9-helix and the β-peptide 12/10-helix belong to “mixed” helices, in which two types of hydrogen bonds with opposite directionality alternate along the helical axis. cis-2-Aminocyclohaxanecarboxylic acid (cis-ACHC) is...

Structural Basis for Control of Bacterial RNA Polymerase Pausing by a Riboswitch and its Ligand

Folding of nascent transcripts can be modulated by the proximal RNA polymerase (RNAP) that carries out their transcription, and vice versa. A pause of RNAP during transcription of a preQ1 riboswitch (que-ePEC) is stabilized by a previously characterized template consensus sequence and the ligand-free conformation of the nascent RNA. Ligand binding to the riboswitch induces RNAP pause release and downstream transcription termination, however, the mechanism by which riboswitch folding modulates pausing is unclear. Here, we report single-particle cryo-electron microscopy reconstructions of que-ePEC in ligand-free and ligand-bound states. In the absence of preQ1, the RNA transcript is in an unexpected hyper-translocated state, preventing downstream nucleotide incorporation. Strikingly, upon ligand binding the riboswitch rotates around its helical axis, expanding the surrounding RNAP exit channel and repositioning the transcript for elongation. Our study reveals the tight coupling by which small nascent RNA structures and their ligands can functionally regulate the macromolecular transcription machinery.

Demonstration of reduced neoclassical energy transport in Wendelstein 7-X

Research on magnetic confinement of high-temperature plasmas has the ultimate goal of harnessing nuclear fusion for the production of electricity. Although the tokamak1 is the leading toroidal magnetic-confinement concept, it is not without shortcomings and the fusion community has therefore also pursued alternative concepts such as the stellarator. Unlike axisymmetric tokamaks, stellarators possess a three-dimensional (3D) magnetic field geometry. The availability of this additional dimension opens up an extensive configuration space for computational optimization of both the field geometry itself and the current-carrying coils that produce it. Such an optimization was undertaken in designing Wendelstein 7-X (W7-X)2, a large helical-axis advanced stellarator (HELIAS), which began operation in 2015 at Greifswald, Germany. A major drawback of 3D magnetic field geometry, however, is that it introduces a strong temperature dependence into the stellarator’s non-turbulent ‘neoclassical’ energy transport. Indeed, such energy losses will become prohibitive in high-temperature reactor plasmas unless a strong reduction of the geometrical factor associated with this transport can be achieved; such a reduction was therefore a principal goal of the design of W7-X. In spite of the modest heating power currently available, W7-X has already been able to achieve high-temperature plasma conditions during its 2017 and 2018 experimental campaigns, producing record values of the fusion triple product for such stellarator plasmas3,4. The triple product of plasma density, ion temperature and energy confinement time is used in fusion research as a figure of merit, as it must attain a certain threshold value before net-energy-producing operation of a reactor becomes possible1,5. Here we demonstrate that such record values provide evidence for reduced neoclassical energy transport in W7-X, as the plasma profiles that produced these results could not have been obtained in stellarators lacking a comparably high level of neoclassical optimization.

The molecular architecture of vimentin filaments

Intermediate filaments are integral components of the cytoskeleton in metazoan cells. Due to their specific viscoelastic properties they are principal contributors to flexibility and tear strength of cells and tissues. Vimentin, an intermediate filament protein expressed in fibroblasts and endothelial cells, assembles into ~11 nm thick biopolymers, that are involved in a wide variety of cellular functions in health and disease. Here, we reveal the structure of in-situ polymerized vimentin filaments to a subnanometer resolution by applying cryo-electron tomography to mouse embryonic fibroblasts grown on electron microscopy grids. We show that vimentin filaments are tube-like assemblies with a well-defined helical symmetry. Their structure is comprised of five octameric, spring-like protofibrils harboring 40 vimentin polypeptide chains in cross-section. The protofibrils are connected by the intrinsically disordered head and helix 1A domains of vimentin. Individual filaments display two polymerization states characterized by either the presence or absence of a luminal density along the helical axis. The structure of vimentin filaments unveils the generic building plan of the intermediate filament superfamily in molecular details.

Why amyloid fibrils have a limited width

Amyloid fibrils can grow indefinitely long by adding protein chains to the tips of the fibril through β–sheet hydrogen bonding; however, they do not grow laterally beyond ~10–20 nm. This prevents amyloid fibrils from growing into two–dimensional or three–dimensional arrays. The forces that restrict lateral association of β–sheets in amyloid fibrils are not immediately apparent. We hypothesize that it is the helical symmetry of amyloid fibrils that imposes the limit on fibril width by incurring an increasing separation between helically related molecules as a function of radial distance from the helical axis. The unavoidable consequence is that backbone hydrogen bonds that connect symmetrically related layers of the fibril become weaker towards the edge of the fibril, ultimately becoming too weak to remain ordered. To test our hypothesis, we examined 57 available cryo-EM amyloid fibril structures for trends in interstrand distance and β–sheet hydrogen bonding as a function of radial distance from the helical axis. We find that all fibril structures display an increase in interstrand distance as a function of radius and that most fibril structures have a discernible increase in β–sheet hydrogen bond distances as a function of radius. In addition, we identify a high resolution cryo–EM structure that does not follow our predicted hydrogen bonding trends and perform real space refinement with hydrogen bond distance and angle restraints to restore predicted hydrogen bond trends. This highlights the potential to use our analysis to ensure realistic hydrogen bonding in amyloid fibrils when atomic resolution cryo–EM maps are not available.

Kinetic-ballooning-mode turbulence in low-average-magnetic-shear equilibria

Kinetic-ballooning-mode (KBM) turbulence is studied via gyrokinetic flux-tube simulations in three magnetic equilibria that exhibit small average magnetic shear: the Helically Symmetric eXperiment (HSX), the helical-axis Heliotron-J and a circular tokamak geometry. For HSX, the onset of KBM being the dominant instability at low wavenumber occurs at a critical value of normalized plasma pressure $\beta ^{\rm KBM}_{\rm crit}$ that is an order of magnitude smaller than the magnetohydrodynamic (MHD) ballooning limit $\beta ^{\rm MHD}_{\rm crit}$ when a strong ion temperature gradient (ITG) is present. However, $\beta ^{\rm KBM}_{\rm crit}$ increases and approaches the MHD ballooning limit as the ITG tends to zero. For these configurations, $\beta ^{\rm KBM}_{\rm crit}$ also increases as the magnitude of the average magnetic shear increases, regardless of the sign of the normalized magnetic shear. Simulations of Heliotron-J and a circular axisymmetric geometry display behaviour similar to HSX with respect to $\beta ^{\rm KBM}_{\rm crit}$ . Despite large KBM growth rates at long wavelengths in HSX, saturation of KBM turbulence with $\beta > \beta _{\rm crit}^{\rm KBM}$ is achievable in HSX and results in lower heat transport relative to the electrostatic limit by a factor of roughly five. Nonlinear simulations also show that KBM transport dominates the dynamics when KBMs are destabilized linearly, even if KBM growth rates are subdominant to ITG growth rates.

Relationship between patellofemoral finite helical axis and femoral trans-epicondylar axis using a static magnetic resonance-based methodology

Background To manage patellofemoral joint disorders, a complete understanding of the in vivo patellofemoral kinematics is critical. However, as one of the parameters of joint kinematics, the location and orientation of the patellofemoral finite helical axis (FHA) remains unclear. The purpose of this study is to quantify the location and orientation of the patellar FHA, both in vivo and non-invasively at various flexion angles, and evaluate the relationship of the FHA and the trans-epicondylar axis (TEA). Methods The magnetic resonance (MR) images of 18 unilateral knees were collected at full extension, 30°, 60°, 90°, and maximum angle of knee flexion. Three-dimensional models of the knee joint at different flexion angles were created using the MR images, and then used to calculate the patellar tracking and FHA with a spline interpolation algorithm. By using a coordinate system based on the TEA, the FHA tracking was quantified. Six parameters concerning the location and orientation of the patellar FHA were analysed. Results The average patellar FHA drew an L-shaped tracking on the midsagittal plane moving from the posteroinferior to the anterosuperior side of the TEA with knee flexion. Before 90° flexion, the patellar rotational radius decreased slightly, with an average value of 5.65 ± 1.09 cm. During 20° to 90° knee flexion, the average angle between the patellar FHA and the TEA was approximately 10° and that between the FHA and the coronal plane was maintained at about 0°, while that between the FHA and the level plane fluctuated between − 10° and 10°. Conclusions This study quantitatively reported the continuous location and direction of the patellar FHA during knee flexion. The patellar FHA was close to but not coincident with the femoral TEA both in location and orientation, and the patellar rotational radius decreased slightly with knee flexion. These findings could provide a clear direction for further studies on the difference in patellofemoral FHA among various types of patellofemoral disorders, and provide a foundation for the application of FHA in surgical evaluation, preoperative planning and prosthesis design, thereby assisting in the diagnosis and treatment of patellofemoral disorders.

Folds induced by multiple parallel or antiparallel double-helices: (pseudo)knotting of single-stranded RNA

ABSTRACTWe develop tools to explore and catalogue the topologies of knotted or pseudoknotted circular folds due to secondary and tertiary interactions within a closed loop of RNA which generate multiple double-helices due (for example) to strand complementarity. The fold topology is captured by a ‘contracted fold’ which merges helices separated by bulges and removes hairpin loops. Contracted folds are either trivial or pseudoknotted. Strand folding is characterised by a rigid-vertex ‘polarised strand graph’, whose vertices correspond to double-helices and edges correspond to strands joining those helices. Each vertex has a plumbline whose polarisation direction defines the helical axis. That polarised graph has a corresponding circular ribbon diagram and canonical alphanumeric fold label. Key features of the ‘fully-flagged’ fold are the arrangement of complementary domains along the strand, described by a numerical bare fold label, and a pair of binary ‘flags’: a parity flag that specifies the twist in each helix (even or odd half-twists), and an orientation flag that characterises each double-helix as parallel or antiparallel. A simple algorithm is presented to translate an arbitrary fold label into a polarised strand graph. Any embedding of the graph in 3-space is an admissible fold geometry; the simplest embeddings minimise the number of edge-crossings in a planar graph drawing. If that number is zero, the fold lies in one of two classes: (a)-type ‘relaxed’ folds, which contain conventional junctions and (b)-type folds whose junctions are described as meso-junctions in H. Wang and N.C. Seeman, Biochem, vol. 34, pp920-929. (c)-type folds induce polarised strand graphs with edge-crossings, regardless of the planar graph drawing. Canonical fold labelling allows us to sort and enumerate all ‘semi-flagged’ folds with up to six contracted double-helices as windings around the edges of a graph-like fold skeleton, whose cyclomatic number - the ‘fold genus’ - ranges from 0 – 3, resulting in a pair of duplexed strands along each skeletal edge. Those semi-flagged folds admit both even and odd double-helical twists. Appending specific parity flags to those semi-flagged folds gives fully-flagged (a)-type folds, which are also enumerated up to genus-3 cases. We focus on all-antiparallel folds, characteristic of conventional ssRNA and enumerate all distinct (a), (b) and (c)-type folds with up to five double-helices. Those circular folds lead to pseudoknotted folds for linear ssRNA strands. We describe all linear folds derived from (a) or (b)-type circular folds with up to four contracted double-helices, whose simplest cases correspond to so-called H, K and L pseudoknotted folds, detected in ssRNA. Fold knotting is explored in detail, via constructions of so-called antifolds and isomorphic folds. We also tabulate fold knottings for (a) and (b)-type folds whose embeddings minimise the number of edge-crossings and outline the procedure for (c)-type folds. The inverse construction - from a specific knot to a suitable nucleotide sequence - results in a hierarchy of knots. A number of specific alternating knots with up to 10 crossings emerge as favoured fold designs for ssRNA, since they are readily constructed as (a)-type all-antiparallel folds.