Changes In Relative Orientation Research Articles

Domain Swapping in Abiotic Foldamers.

Foldamer sequences that adopt tertiary helix-turn-helix folds mediated by helix-helix hydrogen bonding in organic solvents have been previously reported. In an attempt to create genuine abiotic quaternary structures, i.e. assemblies of tertiary structures, new sequences were prepared that possess additional hydrogen bond donors at positions that may promote an association between the tertiary folds. However, a solid state structure and extensive solution state investigations by Nuclear Magnetic Resonance (NMR) and Circular dichroism (CD) show that, instead of forming a quaternary structure, the tertiary folds assemble into stable swapped-domain dimer motifs. Domain swapping entails a complete reorganization of the arrays of hydrogen bonds and changes in relative helix orientation and handedness that can all be rationalized.

Domain Swapping in Abiotic Foldamers

Foldamer sequences that adopt tertiary helix‐turn‐helix folds mediated by helix‐helix hydrogen bonding in organic solvents have been previously reported. In an attempt to create genuine abiotic quaternary structures, i.e. assemblies of tertiary structures, new sequences were prepared that possess additional hydrogen bond donors at positions that may promote an association between the tertiary folds. However, a solid state structure and extensive solution state investigations by Nuclear Magnetic Resonance (NMR) and Circular dichroism (CD) show that, instead of forming a quaternary structure, the tertiary folds assemble into stable swapped‐domain dimer motifs. Domain swapping entails a complete reorganization of the arrays of hydrogen bonds and changes in relative helix orientation and handedness that can all be rationalized.

In situ monitoring of protein transfer into nanoscale channels

Protein transfer into nanoscale compartments is critical for many cellular/life processes, yet there are few reports on how compartment properties impact the protein orientation during a transfer. Such a knowledge gap limits a deeper understanding of the protein transfer mechanism, which could be bridged using nanoporous materials. Here, we use a mesoporous silica, a covalent organic framework, and a metal-organic framework with charged, hydrophobic, and neutral surfaces, respectively, to elucidate the impact of channel properties on the transfer of a model protein, lysozyme. Using site-directed spin labeling and time-resolved electron paramagnetic resonance spectroscopy, we reveal that the transfer can be a multi-step process depending on channel properties and depict the relative orientation changes of lysozyme upon transfer into each channel. To the best of our knowledge, this is the first structural insight into protein orientation upon transfer into different compartments, meaningful for the rational design of synthetic materials to host enzymes or mimic the cellular compartments. Protein transfer into nanoscale channels differing in hydrophobicity is demonstrated Multi-step protein transfer is observed for charged and hydrophobic channels Protein changes its orientation depending on the channel surface properties Time-resolved EPR spectroscopy can reveal residue-level details of protein transfer Pan et al. report the orientation changes of a model protein upon transfer into three nanoscale channels that differ in surface hydrophobicity (but a similar diameter). The findings may be useful for guiding the rational design of synthetic materials to host enzymes and/or mimic the cellular compartments.

Crystal structure of the full‐length LysR‐type transcription regulator CbnR in complex with promoter DNA

LysR-type transcription regulators (LTTRs) comprise one of the largest families of transcriptional regulators in bacteria. They are typically homo-tetrameric proteins and interact with promoter DNA of approximately 50-60 bp. Earlier biochemical studies have suggested that LTTR binding to promoter DNA bends the DNA and, upon inducer binding, the bend angle of the DNA is reduced through a quaternary structure change of the tetrameric LTTR, leading to the activation of transcription. To date, crystal structures of full-length LTTRs, DNA-binding domains with their target DNAs, and the regulatory domains with and without inducer molecules have been reported. However, these crystal structures have not provided direct evidence of the quaternary structure changes of LTTRs or of the molecular mechanism underlying these changes. Here, we report the first crystal structure of a full-length LTTR, CbnR, in complex with its promoter DNA. The crystal structure showed that, in the absence of bound inducer molecules, the four DNA-binding domains of the tetrameric CbnR interact with the promoter DNA, bending the DNA by approximately 70°. Structural comparison between the DNA-free and -bound forms demonstrates that the quaternary structure change of the tetrameric CbnR required for promoter region-binding arises from relative orientation changes of the three domains in each subunit. The mechanism of the quaternary structure change caused by inducer binding is also discussed based on the present crystal structure, affinity analysis between CbnR and the promoter DNA, and earlier mutational studies on CbnR.

Investigation of wind load alteration on rectangular cross-section tall building due to change in relative orientation of interfering building

The alteration of wind pressure distribution caused by the change in relative orientation of a closely located interfering building is studied here on a rectangular cross-sectional shape principal tall building. Interfering building having same cross-sectional shape and height as that of principal building is placed close and in-front of the principal building, with across-wind lengths of two buildings being in-line with each other, keeping one vertical edge of the interfering building in same position the internal angle between principal and interfering building is changed. Two independent type of measurements are undertaken for varying internal angle: (1). Force Measurement (2). Pressure Measurement. For purpose of validation, the results obtained from two independent measurements mentioned are compared later. The results obtained from force measurements are expressed in the form of two-dimensional X-Y plots, while that for pressure measurement are depicted in the form of mean and RMS wind pressure coefficient (CP and CP′) contour plots on all vertical faces of the principal building. It is noted from force measurement, that for internal angle of 00 principal building is fully shielded by the interfering building, in fact a negative drag is observed on the principal building. As the internal angle increases from 00 to 900 the shielding effect caused by the interfering building reduces, as the internal angle further increases from 900 to 1800 a small but uniform increase in along wind force is noted. High magnitudes of across-wind forces and twisting moments are also noted in some cases. Contour plots of mean pressure coefficients give a detailed reason for results obtained with force measurement and also distinctly show the distribution of pressure across vertical faces of the principal building.

Ripple period adjustment on SiC surface based on electron dynamics control and its polarization anisotropy

In this paper, the Mach Zehnder interferometer is utilized to generate a collinear dual optical path with 800-nm center wavelength, 1 kHz repetition rate, 120-fs pulse duration and an energy ratio of 1:1 to scan 6H-SiC crystal at a scanning speed of 500 μm/s, resulting in laser-induced periodic surface structure (LIPSS). From the perspective of instantaneous electron density level, variation of the period of low spatial frequency LIPSS (LSFL) with interpulse delay time and polarization angle is studied. The scanning electron microscope (SEM) characterization of the line-scanned ablation zone combined with fast Fourier transformation (FFT) spectrum analysis shows that the period of LSFL decreases with the increase of delay time, and remains stable when the delay exceeds 240 fs. Meanwhile, the period of LSFL increases with the increase of polarization angle under the same delay time, showing an anisotropy that dependent on the polarization angle. The variation trend of the maximum electron density level with delay time calculated by electron rate equation is roughly consistent with the periodic variation trend. Interaction between incident light and transient metal-like SiC surface is simulated based on finite-difference time-domain method (FDTD). The simulation results show that the surface of the sample has a periodic light field enhancement structure controlled by the transient electron density, which explains the phenomenon that the period decreases with increasing delay time. It is further confirmed that the formation of LSFL is due to the interference of incident light and surface plasmon, and the period of LSFL can be controlled by adjusting the electron density level by delay time. The periodic polarization dependence of LSFL may be related to the relative orientation change of the laser pulse front tilt (PFT) and laser polarization.

Active multiview recognition with hidden Markov temporal support

Our paper deals with active multiview object recognition focusing on the directional support of sequential multiple shots. Since inertial sensors are easily available nowadays, we propose the use of them to estimate the orientation change of the camera and thus to estimate the probability of relative poses. With the help of relative orientation change, we can compute transition probabilities between possible poses and can use a hidden Markov model to evaluate state (pose) sequences and can thus increase the recognition rate. Furthermore, we can plan our next viewing position to minimize the risk of misclassification, resulting in higher overall recognition rates. Besides giving the theoretical details, we use two datasets to illustrate the performance of our model through several tests including occlusion, blur, Gaussian noise, and to compare to a solution with a long short-term memory network.

Analysis and Design of a Robust, Low-Power, Inductively Coupled LSK Data Link

A low-power half-duplex data link transmits data at up to 4 Mb/s over coupled inductors across distances of up to 5 cm. The inductors are part of two resonators which tune a free-running oscillator to one of their natural modes. This gives robustness to changes in coil distance and relative orientation. With load-shift keying (LSK) employed in the remote transponder, the link is modeled analytically to reveal some unexpected properties. A complete design guide aids selection of coil size for range, carrier frequency for data rate, and $Q$ -switching to extend range. Owing to low power circuit design, the remote transponder consumes 0.075 pJ/b in transmit, 5 pJ/b in receive mode.

Experimental Investigation of Linear Encoder’s Subdivisional Errors under Different Scanning Speeds

Optical encoders are widely used in applications requiring precise displacement measurement and fluent motion control. To reach high positioning accuracy and repeatability, and to create a more stable speed-control loop, essential attention must be directed to the subdivisional error (SDE) of the used encoder. This error influences the interpolation process and restricts the ability to achieve a high resolution. The SDE could be caused by various factors, such as the particular design of the reading head and the optical scanning principle, quality of the measuring scale, any kind of relative orientation changes between the optical components caused by mechanical vibrations or deformations, or scanning speed. If the distorted analog signals are not corrected before interpolation, it is very important to know the limitations of the used encoder. The methodology described in this paper could be used to determine the magnitude of an SDE and its trend. This method is based on a constant-speed test and does not require high-accuracy reference. The performed experimental investigation of the standard optical linear encoder SDE under different scanning speeds revealed the linear relationship between the tested encoder’s traversing velocity and the error value. A more detailed investigation of the obtained results was done on the basis of fast Fourier transformation (FFT) to understand the physical nature of the SDE, and to consider how to improve the performance of the encoder.

Probing Relative Domain Mobility of Class-I Major Histocompability Complex Molecules through Residual Dipolar Couplings

The highly polymorphic proteins of class I major histocompatibility complex (MHC-I) are 45 kDa multi-domain heterodimers that play a key role in orchestrating the human adaptive immune response. Their function is to present endogenous and exogenous peptide ligands to cytotoxic T cells and Natural Killer cells. Despite a wealth of X-ray structural information on these proteins and their complexes, dynamic studies by NMR have been restricted to the study of local (chemical shift-based) changes occurring at different timescales, using relaxation experiments recorded for amide probes. Recent work from our group using methyl probes has suggested the presence of an allosteric network on the MHC structure, which is modulated in different alleles with functional consequences for the recognition of peptides and molecular chaperones. However, the precise structural mechanism underlying how conformational changes at the peptide-binding groove induced by the binding of different ligands affect the distal α3 domain remains unclear. Here we have obtained full NMR backbone assignments for a common human MHC-I molecule, HLA-A∗02:01, bound to two different high-affinity peptides. Using transverse relaxation optimized spectroscopy-based methods (ARTSY), we collected residual dipolar couplings (RDCs) for both systems, and utilized this data as restraints for structural refinement towards a rigorous analysis of alignment tensors for the different protein domains, relative to an overall molecular frame. Our results suggest that the local conformation of the peptide-binding groove may affect the global structure of the molecule via subtle changes in relative domain orientation and mobility. Our NMR-based mechanism has important implications for how MHC-I molecules of different peptide occupancies interact with their CD8 co-receptors and molecular chaperones.

Relative Alignment between the Magnetic Field and Molecular Gas Structure in the Vela C Giant Molecular Cloud Using Low- and High-density Tracers

We compare the magnetic field orientation for the young giant molecular cloud Vela C inferred from 500-$\mu$m polarization maps made with the BLASTPol balloon-borne polarimeter to the orientation of structures in the integrated line emission maps from Mopra observations. Averaging over the entire cloud we find that elongated structures in integrated line-intensity, or zeroth-moment maps, for low density tracers such as $^{12}$CO and $^{13}$CO $J$ $\rightarrow$ 1 - 0 are statistically more likely to align parallel to the magnetic field, while intermediate or high density tracers show (on average) a tendency for alignment perpendicular to the magnetic field. This observation agrees with previous studies of the change in relative orientation with column density in Vela C, and supports a model where the magnetic field is strong enough to have influenced the formation of dense gas structures within Vela C. The transition from parallel to no preferred/perpendicular orientation appears to happen between the densities traced by $^{13}$CO and by C$^{18}$O $J$ $\rightarrow$ 1 - 0. Using RADEX radiative transfer models to estimate the characteristic number density traced by each molecular line we find that the transition occurs at a molecular hydrogen number density of approximately $10^3$ cm$^{-3}$. We also see that the Centre-Ridge (the highest column density and most active star-forming region within Vela C) appears to have a transition at a lower number density, suggesting that this may depend on the evolutionary state of the cloud.

On the Prediction of Pantographing that Occurs between Reinforcement Cords Embedded within Uncured Rubber Layers during Molding of Tires

Abstract Molding is a key stage in the manufacturing process of a rubber tire. An unvulcanized tire consists of several layers of rubber compounds, some of which are reinforced with sets of fabric cords or wire cords. The final shape of the tire, including the tread patterns and markings, is obtained after insertion of the tire into a curing mold and inflation with an appropriate pressure. The relative orientation of reinforcements may change during the inflation phase. This relative orientation change is referred to as pantographing, and it will affect the properties of the finished tire. Predicting possible changes of orientation of reinforcements during inflation is therefore useful for subsequent technological assessment.

Outward open conformation of a Major Facilitator Superfamily multidrug/H+ antiporter provides insights into switching mechanism

Multidrug resistance (MDR) poses a major challenge to medicine. A principle cause of MDR is through active efflux by MDR transporters situated in the bacterial membrane. Here we present the crystal structure of the major facilitator superfamily (MFS) drug/H+ antiporter MdfA from Escherichia coli in an outward open conformation. Comparison with the inward facing (drug binding) state shows that, in addition to the expected change in relative orientations of the N- and C-terminal lobes of the antiporter, the conformation of TM5 is kinked and twisted. In vitro reconstitution experiments demonstrate the importance of selected residues for transport and molecular dynamics simulations are used to gain insights into antiporter switching. With the availability of structures of alternative conformational states, we anticipate that MdfA will serve as a model system for understanding drug efflux in MFS MDR antiporters.

Globally Monitoring Allosteric Coupling in the A2A Adenosine Receptor by NMR in Solution

In human G protein‐coupled receptors (GPCRs), drug binding near the extracellular region drives conformational changes over 30 Å away at the intracellular surface, leading to complex formation with partner proteins that initiate signaling. GPCR crystal structures have revealed the need for deeper understanding of conformational dynamics to describe mechanisms of allosteric coupling between the extracellular and intracellular surfaces.Using nuclear magnetic resonance (NMR) in solution, we provide a structural basis for allosteric coupling in the human A2A adenosine receptor (A2AAR), a validated drug target for Parkinson's disease and cancer co‐immunotherapies. Production of A2AAR in Pichia pastoris allowed stable‐isotope labeling with 2H,15N, and 13C, yielding reproducible high‐quality NMR correlation spectra. Assignment of endogenous tryptophans and glycines provided numerous probes distributed over the receptor intracelluar surface, extracellular surface, and transmembrane domain, enabling a global characterization of A2AAR responses to variable efficacy of bound drugs. The “toggle switch” Trp 2466.48 was especially sensitive to variable drug efficacy due to the changes in relative orientation of the nearby aromatic ring of Phe 2426.44 in the highly conserved Pro5.50‐Ile3.40‐Phe6.44 (P‐I‐F) activation motif, providing a highly responsive probe of changes in structure and dynamics upon agonist binding. The novel NMR probes also enabled us to observe ligand efficacy‐related local conformational polymorphisms near the intracellular surface.The distributed NMR probes were utilized to monitor the impact of a key mutation in the A2AAR allosteric center at Asp522.50. Amino acid replacement of Asp522.50 leads to immediate loss of intracellular signaling. In NMR studies, this mutation caused striking changes in conformational polymorphisms at the intracellular surface but did not alter response to drug efficacy at the extracellular surface. We correlated changes at the intracellular surface to structural rearrangements at Trp 2466.48 and the P‐I‐F motif, demonstrating an interplay between the allosteric center and Trp 2466.48, and providing novel insights into a signaling mechanism that may be applicable to a wide range of class A GPCRs.Support or Funding InformationAmerican Cancer Society (MTE)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Cross-device hand vein recognition based on improved SIFT

The recognition rate of SIFT algorithm in single hand vein database has been as high as 99.5%. But with the development of Internet-plus technology, the demand for distributed systems becomes more and more significant. However, the problem of picture quality caused by cross-device makes the intraclass variations larger. For example, when gathering the dorsal hand vein images, subtle changes in relative distance and orientation among the imaging camera, the illumination LED arrays and the different location of users’ hand, as well as shielding by the external housing box from ambient light sources and so on, these will make large difference to one person’s hand images. So, including the contrast, the lightness, the shifting, the angle of rotation, the size and so on, these differences make it possible to use some traditional methods to recognize dorsal hand vein with a low recognition rate of less than 50%. Therefore, based on the traditional SIFT, this paper optimized the scale factor [Formula: see text], extreme searching neighborhood structure and matching threshold [Formula: see text]. It can be seen that the cross-device hand vein feature is more robust, and the recognition rate reached an average of 88.5%.

What are we learning from the relative orientation between density structures and the magnetic field in molecular clouds?

We investigate the conditions of ideal magnetohydrodynamic (MHD) turbulence responsible for the relative orientation between density structures, characterized by their gradient, $\vec{\nabla}\rho$, and the magnetic field, $\vec{B}$, in molecular clouds (MCs). For that purpose, we construct an expression for the time evolution of the angle, $\phi$, between $\vec{\nabla}\rho$ and $\vec{B}$ based on the transport equations of MHD turbulence. Using this expression, we find that the configuration where $\vec{\nabla}\rho$ and $\vec{B}$ are mostly parallel, $\cos\phi=1$, and where $\vec{\nabla}\rho$ and $\vec{B}$ are mostly perpendicular, $\cos\phi=0$, constitute attractors, that is, the system tends to evolve towards either of these configurations and they are more represented than others. This fact would explain the predominant alignment or anti-alignment between column density, $N_H$, structures and the projected magnetic field orientation, $\hat{B}_\perp$, reported in observations. Additionally, we find that departures from the $\cos\phi=0$ configurations are related to convergent flows, quantified by the divergence of the velocity field, $\vec{\nabla}\cdot\vec{v}$, in the presence of a relatively strong magnetic field. This would explain the observed change in relative orientation between $N_H$-structures and $\hat{B}_\perp$ towards MCs, from mostly parallel at low $N_H$ to mostly perpendicular at the highest $N_H$, as the result of the gravitational collapse and/or convergence of flows. Finally, we show that the density threshold that marks the observed change in relative orientation towards MCs, from $N_H$ and $\hat{B}_\perp$ being mostly parallel at low $N_H$ to mostly perpendicular at the highest $N_H$, is related to the magnetic field strength and constitutes a crucial piece of information for determining the role of the magnetic field in the dynamics of MCs.

Computational Investigation into the Solution Structure of Monomeric Lassa Virus Nucleoprotein and Insights into its RNA Binding Mechanism

Lassa is a dangerous Arenavirus, which is enveloped and has a single-stranded (ss)RNA genome. The nucleoprotein (NP) is the most abundant protein in the virion and functions to encapsidate the viral genome to form a ribonucleoprotein complex (RNP). Studies of the full-length NP show it forms a circular trimer and does not bind to RNA. However, a structure of just the N-terminal domain bound to RNA has also been determined, which indicates structural reorganization is required to bind ssRNA. Therefor it is believed that NP must undergo a large conformational change from the observed trimeric configuration in order to bind and polymerize on ssRNA to form the RNP.Using molecular dynamics and metadynamics simulations we have investigated the influence of RNA on the global motions of the N-terminal domain of Lassa NP, and have identified that RNA-binding reduces the free energy barrier to transition to the RNA bound state. We have gone on to investigate the conformational dynamics of the full-length NP in apo and RNA bound states when free in solution as a monomer. During multi-microsecond MD simulations performed on the Anton supercomputer, we observed significant conformational changes in the NP. In both apo and RNA bound simulations, we observe changes in interdomain contacts and relative domain orientation, as well formation of helical secondary structure in an unresolved domain linker loop. Most notably in the RNA bound simulation, the domain orientation is much more dramatic, and provides a putative template to understand the higher-order structural organization of the RNP. Kinetic network analysis and Brownian dynamics simulations have been employed to further analyze the structural transition pathways and to evaluate mechanisms of transition from the RNA-free trimer to the RNP.

Intra-operative measurement of applied forces during anterior scoliosis correction

BackgroundSpinal instrumentation and fusion for the treatment of scoliosis is primarily a mechanical intervention to correct the deformity and halt further progression. While implant-related complications remain a concern, little is known about the magnitudes of the forces applied to the spine during surgery, which may affect post-surgical outcomes. In this study, the compressive forces applied to each spinal segment during anterior instrumentation were measured in a series of patients with Adolescent Idiopathic Scoliosis. MethodsA force transducer was designed and retrofit to a routinely used surgical tool, and compressive forces applied to each segment during surgery were measured for 15 scoliosis patients. Cobb angle correction achieved by each force was measured on intra-operative fluoroscope images. Relative changes in orientation of the screw within the vertebra were also measured to detect intra-operative screw plough. FindingsIntra-operative forces were measured for a total of 95 spinal segments. The mean applied compressive force was 540N (SD 230N, range 88N–1019N). There was a clear trend for higher forces to be applied at segments toward the apex of the scoliosis. Fluoroscopic evidence of screw plough was detected at 10 segments (10.5%). InterpretationThe magnitude of forces applied during anterior scoliosis correction vary over a broad range. These forces do reach magnitudes capable of causing intra-operative vertebral body screw plough. Surgeons should be aware there is a risk for tissue overload during correction, however the clinical implications of intra-operative screw plough remain unclear. The dataset presented here is valuable for providing realistic input parameters for in silico surgical simulations.

Impact of Molecular Orientation and Packing Density on Electronic Polarization in the Bulk and at Surfaces of Organic Semiconductors.

The polarizable environment surrounding charge carriers in organic semiconductors impacts the efficiency of the charge transport process. Here, we consider two representative organic semiconductors, tetracene and rubrene, and evaluate their polarization energies in the bulk and at the organic-vacuum interface using a polarizable force field that accounts for induced-dipole and quadrupole interactions. Though both oligoacenes pack in a herringbone motif, the tetraphenyl substituents on the tetracene backbone of rubrene alter greatly the nature of the packing. The resulting change in relative orientations of neighboring molecules is found to reduce the bulk polarization energy of holes in rubrene by some 0.3 eV when compared to tetracene. The consideration of model organic-vacuum interfaces highlights the significant variation in the electrostatic environment for a charge carrier at a surface although the net change in polarization energy is small; interestingly, the environment of a charge even just one layer removed from the surface can be viewed already as representative of the bulk. Overall, it is found that in these herringbone-type layered crystals the polarization energy has a much stronger dependence on the intralayer packing density than interlayer packing density.

Planckintermediate results

Within ten nearby (d < 450 pc) Gould Belt molecular clouds we evaluate statistically the relative orientation between the magnetic field projected on the plane of sky, inferred from the polarized thermal emission of Galactic dust observed by Planck at 353 GHz, and the gas column density structures, quantified by the gradient of the column density, $N_H$. The selected regions, covering several degrees in size, are analyzed at an effective angular resolution of 10' FWHM, thus sampling physical scales from 0.4 to 40 pc in the nearest cloud. The column densities in the selected regions range from $N_H \approx 10^{21}$ to $10^{23}$ cm$^{-2}$, and hence they correspond to the bulk of the molecular clouds. The relative orientation is evaluated pixel by pixel and analyzed in bins of column density using the novel statistical tool called "Histogram of Relative Orientations". Throughout this study, we assume that the polarized emission observed by Planck at 353 GHz is representative of the projected morphology of the magnetic field in each region, i.e., we assume a constant dust grain alignment efficiency, independent of the local environment. Within most clouds we find that the relative orientation changes progressively with increasing $N_H$, from preferentially parallel or having no preferred orientation to preferentially perpendicular. In simulations of magnetohydrodynamic turbulence in molecular clouds this trend in relative orientation is a signature of Alfv\'enic or sub-Alfv\'enic turbulence, implying that the magnetic field is significant for the gas dynamics at the scales probed by Planck. We compare the deduced magnetic field strength with estimates we obtain from other methods and discuss the implications of the Planck observations for the general picture of molecular cloud formation and evolution.