200 research outputs found

    Redistribution of Flexibility in Stabilizing Antibody Fragment Mutants Follows Le Chatelier's Principle

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    Le Châtelier's principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Châtelier's principle states that an equilibrium shift will occur to offset the perturbation and a new equilibrium is established. We demonstrate that the effects of stabilizing mutations on the rigidity ⇔ flexibility equilibrium within the native state ensemble manifest themselves through enthalpy-entropy compensation as the protein structure adjusts to restore the global balance between the two. Specifically, we characterize the effects of mutation to single chain fragments of the anti-lymphotoxin-β receptor antibody using a computational Distance Constraint Model. Statistically significant changes in the distribution of both rigidity and flexibility within the molecular structure is typically observed, where the local perturbations often lead to distal shifts in flexibility and rigidity profiles. Nevertheless, the net gain or loss in flexibility of individual mutants can be skewed. Despite all mutants being exclusively stabilizing in this dataset, increased flexibility is slightly more common than increased rigidity. Mechanistically the redistribution of flexibility is largely controlled by changes in the H-bond network. For example, a stabilizing mutation can induce an increase in rigidity locally due to the formation of new H-bonds, and simultaneously break H-bonds elsewhere leading to increased flexibility distant from the mutation site via Le Châtelier. Increased flexibility within the VH β4/β5 loop is a noteworthy illustration of this long-range effect

    Fermi surface of the colossal magnetoresistance perovskite La_{0.7}Sr_{0.3}MnO_{3}

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    Materials that exhibit colossal magnetoresistance (CMR) are currently the focus of an intense research effort, driven by the technological applications that their sensitivity lends them to. Using the angular correlation of photons from electron-positron annihilation, we present a first glimpse of the Fermi surface of a material that exhibits CMR, supported by ``virtual crystal'' electronic structure calculations. The Fermi surface is shown to be sufficiently cubic in nature that it is likely to support nesting.Comment: 5 pages, 5 PS figure

    Direct reaction measurements with a 132Sn radioactive ion beam

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    The (d,p) neutron transfer and (d,d) elastic scattering reactions were measured in inverse kinematics using a radioactive ion beam of 132Sn at 630 MeV. The elastic scattering data were taken in a region where Rutherford scattering dominated the reaction, and nuclear effects account for less than 8% of the cross section. The magnitude of the nuclear effects was found to be independent of the optical potential used, allowing the transfer data to be normalized in a reliable manner. The neutron-transfer reaction populated a previously unmeasured state at 1363 keV, which is most likely the single-particle 3p1/2 state expected above the N=82 shell closure. The data were analyzed using finite range adiabatic wave calculations and the results compared with the previous analysis using the distorted wave Born approximation. Angular distributions for the ground and first excited states are consistent with the previous tentative spin and parity assignments. Spectroscopic factors extracted from the differential cross sections are similar to those found for the one neutron states beyond the benchmark doubly-magic nucleus 208Pb.Comment: 22 pages, 7 figure

    Nesting properties and anisotropy of the Fermi surface of LuNi2_{2}B2_{2}C

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    The rare earth nickel borocarbides, with the generic formula RRNi2_{2}B2_{2}C, have recently been shown to display a rich variety of phenomena. Most striking has been the competition between, and even coexistence of, antiferromagnetism and superconductivity. We have measured the Fermi surface (FS) of LuNi2_{2}B2_{2}C, and shown that it possesses nesting features capable of explaining some of the phenomena experimentally observed. In particular, it had previously been conjectured that a particular sheet of FS is responsible for the modulated magnetic structures manifest in some of the series. We report the first direct experimental observation of this sheet.Comment: 4 pages, 4 PS figure

    The magic nature of 132Sn explored through the single-particle states of 133Sn

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    Atomic nuclei have a shell structure where nuclei with 'magic numbers' of neutrons and protons are analogous to the noble gases in atomic physics. Only ten nuclei with the standard magic numbers of both neutrons and protons have so far been observed. The nuclear shell model is founded on the precept that neutrons and protons can move as independent particles in orbitals with discrete quantum numbers, subject to a mean field generated by all the other nucleons. Knowledge of the properties of single-particle states outside nuclear shell closures in exotic nuclei is important for a fundamental understanding of nuclear structure and nucleosynthesis (for example the r-process, which is responsible for the production of about half of the heavy elements). However, as a result of their short lifetimes, there is a paucity of knowledge about the nature of single-particle states outside exotic doubly magic nuclei. Here we measure the single-particle character of the levels in 133Sn that lie outside the double shell closure present at the short-lived nucleus 132Sn. We use an inverse kinematics technique that involves the transfer of a single nucleon to the nucleus. The purity of the measured single-particle states clearly illustrates the magic nature of 132Sn.Comment: 19 pages, 5 figures and 4 table

    Calculating Ensemble Averaged Descriptions of Protein Rigidity without Sampling

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    Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently calculated using the integer body-bar Pebble Game (PG) algorithm. However, thermodynamic properties require averaging over many samples from the ensemble of accessible conformations to accurately account for fluctuations in network topology. We have developed a mean field Virtual Pebble Game (VPG) that represents the ensemble of networks by a single effective network. That is, all possible number of distance constraints (or bars) that can form between a pair of rigid bodies is replaced by the average number. The resulting effective network is viewed as having weighted edges, where the weight of an edge quantifies its capacity to absorb degrees of freedom. The VPG is interpreted as a flow problem on this effective network, which eliminates the need to sample. Across a nonredundant dataset of 272 protein structures, we apply the VPG to proteins for the first time. Our results show numerically and visually that the rigidity characterizations of the VPG accurately reflect the ensemble averaged properties. This result positions the VPG as an efficient alternative to understand the mechanical role that chemical interactions play in maintaining protein stability

    New Constraints on the 18F(p,alpha) 15O Rate in Novae from the (d,p) Reaction

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    The degree to which the (p,gamma) and (p,alpha) reactions destroy 18F at temperatures 1-4x10^8 K is important for understanding the synthesis of nuclei in nova explosions and for using the long-lived radionuclide 18F, a target of gamma-ray astronomy, as a diagnostic of nova mechanisms. The reactions are dominated by low-lying proton resonances near the 18F+p threshold (E_x=6.411 MeV in 19Ne). To gain further information about these resonances, we have used a radioactive 18F beam from the Holifield Radioactive Ion Beam Facility to selectively populate corresponding mirror states in 19F via the inverse d(18F,p)19F neutron transfer reaction. Neutron spectroscopic factors were measured for states in 19F in the excitation energy range 0-9 MeV. Widths for corresponding proton resonances in 19Ne were calculated using a Woods-Saxon potential. The results imply significantly lower 18F(p,gamma)19Ne and 18F(p,alpha)15O reaction rates than reported previously, thereby increasing the prospect of observing the 511-keV annihilation radiation associated with the decay of 18F in the ashes ejected from novae.Comment: Error involving sum rule was corrected. Proton widths were recalculated using a Woods-Saxon potential. Both low-lying resonances (8- and 38-keV) are now included in the rate band. 12 pages, 4 figures, 1 table. Submitted to Phys. Rev.
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