Weak points of antiparallel {beta}-sheets. How are they filled up in globular proteins?

A lack of knowledge about the construction of tight packingis now the main obstacle for a successful design of artificialproteins. In this paper we examine a way of close packing antiparallelß-sandwihes. We show that there are some ‘weakpoints’ at the surfaces of ß-sheets, which cannotbe filled by the surrounding aliphatic side chains that arethe most abundant. Theoretically, these ‘weak points‘can be filled either by aromatic side chains of the same sheetor by the residues of the other parts of the protein molecule.The analysis of protein structures shows that both possibilitiesare used by nature and that there are many cases when these‘weak points’ are not filled by any atom. They remainfree and form a majority of the defects of close packing inprotein globules.     

Importance of an N-terminal extension in ribonuclease HII from Bacillus stearothermophilus for substrate binding

The gene encoding ribonuclease HII from Bacillus stearothermophilus was cloned and expressed in Escherichia coli. The overproduced protein, Bst-RNase HII, was purified and biochemically characterized. Bst-RNase HII, which consists of 259 amino acid residues, showed the highest amino acid sequence identity (50.2%) to Bacillus subtilis RNase HII. Like B. subtilis RNase HII, it exhibited Mn2+-dependent RNase H activity. It was, however, more thermostable than B. subtilis RNase HII. When the Bst-RNase HII amino acid sequence is compared with that of Thermococcus kodakaraensis RNase HII, to which it shows 29.8% identity, 30 residues are observed to be truncated from the C-terminus and there is an extension of 71 residues at the N-terminus. The C-terminal truncation results in the loss of the alpha9 helix, which is rich in basic amino acid residues and is therefore important for substrate binding. A truncated protein, Delta59-Bst-RNase HII, in which most of the N-terminal extension was removed, completely lost its RNase H activity. Surface plasmon resonance analysis indicated that this truncated protein did not bind to the substrate. These results suggest that the N-terminal extension of Bst-RNase HII is important for substrate binding. Because B. subtilis RNase HII has an N-terminal extension of the same length and these extensions contain a region in which basic amino acid residues are clustered, the Bacillus enzymes may represent a novel type of RNase H which possesses a substrate-binding domain at the N-terminus.     

Role of repetitive nine-residue sequence motifs in secretion, enzymatic activity, and protein conformation of a family I.3 lipase

A family I.3 lipase from Pseudomonas sp. MIS38 (PML) contains 12 repeats of a nine-residue sequence motif in the C-terminal region. To elucidate the role of these repetitive sequences, mutant proteins PML5, PML4, PML1, and PML0, in which 7, 8, 11, and all 12 of the repetitive sequences are deleted, and PMLdelta19, in which 19 C-terminal residues are truncated, were constructed. Escherichia coli DH5 cells carrying the Serratia marcescens Lip system permitted the secretion of the wild-type and all of the mutant proteins except for PMLdelta19, although they were partially accumulated in the cells in an insoluble form as well. Both the secretion level and cellular content of the proteins decreased in the order PML > PML5 > PML4 > PML1 > PML0, indicating that repetitive sequences are not required for secretion of PML but are important for its stability in the cells. All the mutant proteins were purified in a refolded form and their biochemical properties were characterized. CD spectra, the Ca2+ contents, and susceptibility to chymotryptic digestion strongly suggested that the five repetitive sequences remaining in PML5 are sufficient to form a beta-roll structure, whereas the four in PML4 are not. PML5 and PMLdelta19 showed both lipase and esterase activities, whereas PML4, PML1, and PML0 were inactive. These results suggest that the enzymatic activity of PML is not seriously affected by a deletion or truncation at the C-terminal region as long as a succession of repetitive sequences can build a beta-roll structure.     

Monte Carlo simulation of microparticle motion in vacuum gap

Breakdown voltages of vacuum gaps become lower when the gaps are contaminated by metallic and ceramic microparticles. In this paper, the motion of the microparticles in the gap is simulated using Monte Carlo method in order to evaluate the effect of parameters upon motion and the removal time of the microparticles. As the parameters, we focused on the material of the microparticle, the frequency, the peak value of the applied voltage, the gap length, and the diameter of the lower and upper electrodes. It turned out that the maximum time needed to remove all microparticles could be expressed as multiple regression function. It is suggested that the reliability of the microparticle removal can be increased by spark conditioning with opening/closing operation.     

NIR-shielding films based on PEDOT-PSS/polysiloxane and polysilsesquioxane hybrid

Near-infrared (NIR)-shielding films based on polysiloxane or polysilsesquioxanes and poly(3,4-ethylenedioxythiophene)-poly(4-styrene sulfonate) (PEDOT-PSS) were synthesized via a sol–gel reaction. Phase-separated mixtures of tetraethyl orthosilicate (TEOS) or methyltriethoxysilane (MTES) with an aqueous dispersion of PEDOT-PSS formed deep-blue homogeneously dispersed sols after stirring. Thin films were prepared by depositing the resulting homogeneously dispersed sols on a glass substrate by spin coating and heating. PEDOT-PSS/TEOS films maintained uniform flat surfaces after 10 coatings. MTES-based films exhibited mottled patterns with nonuniform surfaces. The 10-layer TEOS-based film has high NIR-shielding properties with moderately visible transmittance. NIR absorption by the PEDOT-PSS/TEOS hybrid suppresses air temperature elevation. The five-layer TEOS-based film showed similar NIR-shielding ability and slightly lower visible light transmittance compared with tin-doped indium oxide glass. The 10-layer TEOS-based film exhibited a 15.6% lower temperature rise than the uncoated glass substrate. Specifically, this is an environmentally friendly NIR-shielding material. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2020 , 137, 48367.     

Electrical conductivities of M3P2O8 (M = Ca,Ba)

Two-probe conductivity measurements made for M₃P₂O₈ (M = Ca, Ba) suggested that the electrical conduction of these phosphates would primarily be due to the migration of Ca²⁺ and Ba²⁺ ions. At relatively low temperatures and high oxygen partial pressures, in contrast to Ca₃P₂O₈, however, Ba₃P₂O₈ shows partial electronic conduction.     

Hydrogen reduction in GaAsN thin films by flow rate modulated chemical beam epitaxy

The amount of residual H in the GaAsN film grown by chemical beam epitaxy (CBE) can be decreased by flow rate modulation growth. Many H atoms in the films grown by CBE exist as N-H or N-H₂ structures. Although a higher growth temperature was required for decreasing the H concentration ([H]), it caused a decrease in the N concentration ([N]). A reduction in [H] while keeping [N] constant was necessary. By providing an intermittent supply of Ga source while continuously supplying As and N sources, [H] effectively decreased in comparison with the [H] value in the film grown at the same temperature by conventional CBE without reducing [N].     

A study on the tie‐set graph theory and network flow optimization problems

Aiming at establishing a firm basic theory to ring‐based information network management systems, our paper proposes a tie‐set graph theory. We define a binary vector representing a tie‐set in a biconnected undirected graph G=(V,E) as a tie‐set vector. The set of tie‐set vectors forms a vector space over the proposed law of composition, then a basis of the vector space, μ linear independent tie‐set vectors, is defined as a tie‐set basis. The essential key concept in our theory is a tie‐set graph, which has a one‐to‐one correspondence to a tie‐set basis and represents a relation between two tie‐set vectors of the basis. Some important properties of tie‐set graphs and their application to survivable mesh networks in modern high‐speed backbone networks are also presented. Furthermore, as a general approach to network flow optimization problems, tie‐set flow vector space is proposed based on the tie‐set graph theory. A distributed algorithm for the network flow optimization problems and its application are also presented in this paper. Copyright © 2004 John Wiley & Sons, Ltd.