309 research outputs found

    Electronic Circular Dichroism Spectroscopy of Proteins

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    Circular dichroism (CD) is an important spectroscopic technique that enables the characterization of protein secondary and tertiary structure. Proteins can undergo changes in their structure when they participate in processes, for example, ligand binding. CD, therefore, can be used to monitor secondary and tertiary structural changes when a protein (receptor) binds to a drug molecule (ligand).This review describes experimental studies of protein CD and theoretical and computational methods that compute spectra from structure or structure from spectra. CD is a technique that can be used to complement X-ray, NMR, and ultraviolet-visible (UV-vis) experiments on biomolecules and proteins, all of which can be assisted by molecular modeling, which has the capability of computing CD from first principles. A combination of experimental CD and molecular modeling has the capacity to greatly enhance future multi-disciplinary research to expand our knowledge of the structure, function, and dynamics of proteins

    Membranes in rod solutions: a system with spontaneously broken symmetry

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    We consider a dilute solution of infinitely rigid rods near a curved, perfectly repulsive surface and study the contribution of the rod depletion layer to the bending elastic constants of membranes. We find that a spontaneous curvature state can be induced by exposure of BOTH sides of the membrane to a rod solution. A similar result applies for rigid disks with a diameter equal to the rod's length. We also study the confinement of rods in spherical and cylindrical repulsive shells. This helps elucidate a recent discussion on curvature effects in confined quantum mechanical and polymer systems.Comment: 10 pages, 2 figures, 1 table; submitted to PR

    Tactile Language for a Head-Mounted Sensory Augmentation Device

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    Sensory augmentation is one of the most exciting domains for research in human-machine biohybridicity. The current paper presents the design of a 2nd generation vibrotactile helmet as a sensory augmentation prototype that is being developed to help users to navigate in low visibility environments. The paper outlines a study in which the user navigates along a virtual wall whilst the position and orientation of the user’s head is tracked by a motion capture system. Vibrotactile feedback is presented according to the user’s distance from the virtual wall and their head orientation. The research builds on our previous work by developing a simplified “tactile language” for communicating navigation commands. A key goal is to identify language tokens suitable to a head-mounted tactile interface that are maximally informative, minimize information overload, intuitive, and that have the potential to become ‘experientially transparent

    Seeing ‘Where’ through the Ears: Effects of Learning-by-Doing and Long-Term Sensory Deprivation on Localization Based on Image-to-Sound Substitution

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    BACKGROUND: Sensory substitution devices for the blind translate inaccessible visual information into a format that intact sensory pathways can process. We here tested image-to-sound conversion-based localization of visual stimuli (LEDs and objects) in 13 blindfolded participants. METHODS AND FINDINGS: Subjects were assigned to different roles as a function of two variables: visual deprivation (blindfolded continuously (Bc) for 24 hours per day for 21 days; blindfolded for the tests only (Bt)) and system use (system not used (Sn); system used for tests only (St); system used continuously for 21 days (Sc)). The effect of learning-by-doing was assessed by comparing the performance of eight subjects (BtSt) who only used the mobile substitution device for the tests, to that of three subjects who, in addition, practiced with it for four hours daily in their normal life (BtSc and BcSc); two subjects who did not use the device at all (BtSn and BcSn) allowed assessment of its use in the tasks we employed. The impact of long-term sensory deprivation was investigated by blindfolding three of those participants throughout the three week-long experiment (BcSn, BcSn/c, and BcSc); the other ten subjects were only blindfolded during the tests (BtSn, BtSc, and the eight BtSt subjects). Expectedly, the two subjects who never used the substitution device, while fast in finding the targets, had chance accuracy, whereas subjects who used the device were markedly slower, but showed much better accuracy which improved significantly across our four testing sessions. The three subjects who freely used the device daily as well as during tests were faster and more accurate than those who used it during tests only; however, long-term blindfolding did not notably influence performance. CONCLUSIONS: Together, the results demonstrate that the device allowed blindfolded subjects to increasingly know where something was by listening, and indicate that practice in naturalistic conditions effectively improved "visual" localization performance

    Sensory substitution information informs locomotor adjustments when walking through apertures

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    The study assessed the ability of the central nervous system (CNS) to use echoic information from sensory substitution devices (SSDs) to rotate the shoulders and safely pass through apertures of different width. Ten visually normal participants performed this task with full vision, or blindfolded using an SSD to obtain information regarding the width of an aperture created by two parallel panels. Two SSDs were tested. Participants passed through apertures of +0%, +18%, +35%, and +70% of measured body width. Kinematic indices recorded movement time, shoulder rotation, average walking velocity across the trial, peak walking velocities before crossing, after crossing and throughout a whole trial. Analyses showed participants used SSD information to regulate shoulder rotation, with greater rotation associated with narrower apertures. Rotations made using an SSD were greater compared to vision, movement times were longer, average walking velocity lower and peak velocities before crossing, after crossing and throughout the whole trial were smaller, suggesting greater caution. Collisions sometimes occurred using an SSD but not using vision, indicating that substituted information did not always result in accurate shoulder rotation judgements. No differences were found between the two SSDs. The data suggest that spatial information, provided by sensory substitution, allows the relative position of aperture panels to be internally represented, enabling the CNS to modify shoulder rotation according to aperture width. Increased buffer space indicated by greater rotations (up to approximately 35% for apertures of +18% of body width), suggests that spatial representations are not as accurate as offered by full vision

    Polymer Flow Through Porous Media: Numerical Prediction of the Contribution of Slip to the Apparent Viscosity.

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    The flow of polymer solutions in porous media is often described using Darcy’s law with an apparent viscosity capturing the observed thinning or thickening effects. While the macroscale form is well accepted, the fundamentals of the pore-scale mechanisms, their link with the apparent viscosity, and their relative influence are still a matter of debate. Besides the complex effects associated with the rheology of the bulk fluid, the flow is also deeply influenced by the mechanisms occurring close to the solid/liquid interface, where polymer molecules can arrange and interact in a complex manner. In this paper, we focus on a repulsive mechanism, where polymer molecules are pushed away from the interface, yielding a so-called depletion layer in the vicinity of the wall. This depletion layer acts as a lubricating film that may be represented by an effective slip boundary condition. Here, our goal is to provide a simple mean to evaluate the contribution of this slip effect to the apparent viscosity. To do so, we solve the pore-scale flow numerically in idealized porous media with a slip length evaluated analytically in a tube. Besides its simplicity, the advantage of our approach is also that it captures relatively well the apparent viscosity obtained from core-flood experiments, using only a limited number of inputs. Therefore, it may be useful in many applications to rapidly estimate the influence of the depletion layer effect over the macroscale flow and its relative contribution compared to other phenomena, such as non-Newtonian effects

    HpaC Controls Substrate Specificity of the Xanthomonas Type III Secretion System

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    The Gram-negative bacterial plant pathogen Xanthomonas campestris pv. vesicatoria employs a type III secretion (T3S) system to inject bacterial effector proteins into the host cell cytoplasm. One essential pathogenicity factor is HrpB2, which is secreted by the T3S system. We show that secretion of HrpB2 is suppressed by HpaC, which was previously identified as a T3S control protein. Since HpaC promotes secretion of translocon and effector proteins but inhibits secretion of HrpB2, HpaC presumably acts as a T3S substrate specificity switch protein. Protein–protein interaction studies revealed that HpaC interacts with HrpB2 and the C-terminal domain of HrcU, a conserved inner membrane component of the T3S system. However, no interaction was observed between HpaC and the full-length HrcU protein. Analysis of HpaC deletion derivatives revealed that the binding site for the C-terminal domain of HrcU is essential for HpaC function. This suggests that HpaC binding to the HrcU C terminus is key for the control of T3S. The C terminus of HrcU also provides a binding site for HrpB2; however, no interaction was observed with other T3S substrates including pilus, translocon and effector proteins. This is in contrast to HrcU homologs from animal pathogenic bacteria suggesting evolution of distinct mechanisms in plant and animal pathogenic bacteria for T3S substrate recognition
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