Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like protease cause different conformational changes in crystal structure

AbstractThe 3C-like protease of SARS coronavirus (SARS-CoV 3CLpro) is vital for SARS-CoV replication and is a promising drug target. It has been extensively proved that only the dimeric enzyme is active. Here we discovered that two adjacent mutations (Ser139_Ala and Phe140_Ala) on the dimer interface resulted in completely different crystal structures of the enzyme, demonstrating the distinct roles of these two residues in maintaining the active conformation of SARS-CoV 3CLpro. S139A is a monomer that is structurally similar to the two reported monomers G11A and R298A. However, this mutant still retains a small fraction of dimer in solution, which might account for its remaining activity. F140A is a dimer with the most collapsed active pocket discovered so far, well-reflecting the stabilizing role of this residue. Moreover, a plausible dimerization mechanism was also deduced from structural analysis. Our work is expected to provide insight on the dimerization–function relationship of SARS-CoV 3CLpro

Evolution of hydrogen and helium co-implanted single-crystal silicon during annealing

H+H+ was implanted into single-crystal silicon with a dose of 1×1016/cm21×1016/cm2 and an energy of 30 KeV, and then He+He+ was implanted into the same sample with the same dose and an energy of 33 KeV. Both of the implantations were performed at room temperature. Subsequently, the samples were annealed in a temperature range from 200 to 450 °C450 °C for 1 h. Cross-sectional transmission electron microscopy, Rutherford backscattering spectrometry/channeling, elastic recoil detection, and high resolution x-ray diffraction were employed to characterize the strain, defects, and the distribution of H and He in the samples. The results showed that co-implantation of H and He decreases the total implantation dose, with which the surface could exfoliate during annealing. During annealing, the distribution of hydrogen did not change, but helium moved deeper and its distribution became sharper. At the same time, the maximum of the strain in the samples decreased a lot and also moved deeper. Furthermore, the defects introduced by ion implantation and annealing were characterized by slow positron annihilation spectroscopy, and two positron trap peaks were found. After annealing, the maximum of these two peaks decreased at the same time and their positions moved towards the surface. No bubbles or voids but cracks and platelets were observed by cross-sectional transmission electron microscopy. Finally, the relationship between the total implantation dose and the fraction of hydrogen in total implantation dose was calculated. © 2001 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70387/2/JAPIAU-90-8-3780-1.pd

Comparison between the different implantation orders in H + and He + coimplantation

H + and He + were implanted into single crystals in different orders (H + first or He + first). Subsequently, the samples were annealed at different temperatures from 200 °C to 450 °C for 1 h. Cross sectional transmission electron microscopy, Rutherford backscattering spectrometry and channelling, elastic recoil detection were employed to characterize the defects and the distribution of H and He in the samples. Furthermore, the positron traps introduced by ion implantation and annealing were characterized by slow positron annihilation spectroscopy. Both orders in the coimplantation of H and He have the ability to decreases the total implantation dose after annealing. No bubbles or voids but cracks and platelets, were observed by cross sectional transmission electron microscopy. The different implantation orders affect the density of interstitial atoms and positron traps.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/48910/2/d10406.pd

Emissive Platinum(II) Cages with Reverse Fluorescence Resonance Energy Transfer for Multiple Sensing

It is quite challenging to realize fluorescence resonance energy transfer (FRET) between two chromophores with specific positions and directions. Herein, through the self-assembly of two carefully selected fluorescent ligands via metal-coordination interactions, we prepared two tetragonal prismatic platinum(II) cages with a reverse FRET process between their faces and pillars. Bearing different responses to external stimuli, these two emissive ligands are able to tune the FRET process, thus making the cages sensitive to solvents, pressure, and temperature. First, these cages could distinguish structurally similar alcohols such as n-butanol, t-butanol, and i-butanol. Furthermore, they showed decreased emission with bathochromic shifts under high pressure. Finally, they exhibited a remarkable ratiometric response to temperature over a wide range (223–353 K) with high sensitivity. For example, by plotting the ratio of the maximum emission (I600/I480) of metallacage 4b against the temperature, the slope reaches 0.072, which is among the highest values for ratiometric fluorescent thermometers reported so far. This work not only offers a strategy to manipulate the FRET efficiency in emissive supramolecular coordination complexes but also paves the way for the future design and preparation of smart emissive materials with external stimuli responsiveness

A Chaperonin Subunit with Unique Structures Is Essential for Folding of a Specific Substrate

Type I chaperonins are large, double-ring complexes present in bacteria (GroEL), mitochondria (Hsp60), and chloroplasts (Cpn60), which are involved in mediating the folding of newly synthesized, translocated, or stress-denatured proteins. In Escherichia coli, GroEL comprises 14 identical subunits and has been exquisitely optimized to fold its broad range of substrates. However, multiple Cpn60 subunits with different expression profiles have evolved in chloroplasts. Here, we show that, in Arabidopsis thaliana, the minor subunit Cpn60β4 forms a heterooligomeric Cpn60 complex with Cpn60α1 and Cpn60β1–β3 and is specifically required for the folding of NdhH, a subunit of the chloroplast NADH dehydrogenase-like complex (NDH). Other Cpn60β subunits cannot complement the function of Cpn60β4. Furthermore, the unique C-terminus of Cpn60β4 is required for the full activity of the unique Cpn60 complex containing Cpn60β4 for folding of NdhH. Our findings suggest that this unusual kind of subunit enables the Cpn60 complex to assist the folding of some particular substrates, whereas other dominant Cpn60 subunits maintain a housekeeping chaperonin function by facilitating the folding of other obligate substrates

Regularized Semi-supervised Classification on Manifold

Abstract. Semi-supervised learning gets estimated marginal distribution X P with a large number of unlabeled examples and then constrains the conditional probability ) | ( x y p with a few labeled examples. In this paper, we focus on a regularization approach for semi-supervised classification. The label information graph is first defined to keep the pairwise label relationship and can be incorporated with neighborhood graph which reflects the intrinsic geometry structure of X P . Then we propose a novel regularized semi-supervised classification algorithm, in which the regularization term is based on the modified Graph Laplacian. By redefining the Graph Laplacian, we can adjust and optimize the decision boundary using the labeled examples. The new algorithm combines the benefits of both unsupervised and supervised learning and can use unlabeled and labeled examples effectively. Encouraging experimental results are presented on both synthetic and real world datasets