On-the-fly training of polynomial machine learning potentials in computing lattice thermal conductivity.

The application of first-principles calculations for predicting lattice thermal conductivity (LTC) in crystalline materials, in conjunction with the linearized phonon Boltzmann equation, has gained increasing popularity. In this calculation, the determination of force constants through first-principles calculations is critical for accurate LTC predictions. For material exploration, performing first-principles LTC calculations in a high-throughput manner is now expected, although it requires significant computational resources.

Structure search method for atomic clusters based on the dividing rectangles algorithm.

The Dividing Rectangles (DIRECT) algorithm is a deterministic optimization method to explore optimal solutions by repeatedly dividing a given hyperrectangle search space into subhyperrectangles. Herein, we propose a structure search method for atomic clusters based on the DIRECT algorithm in combination with a gradient-based local optimizer to enable an efficient structure search in high-dimensional search spaces. We use the Z-matrix representation for defining the hyperrectangle search space, in which the bond lengths, bond angles, and dihedral angles specify a cluster structure.

Tracing innovation pathways behind fisheries co-management in Vanuatu.

Co-management approaches have become a core part of coastal fisheries policy and planning practice in Vanuatu. With a long history of supporting community based fisheries management (CBFM), we trace its evolution in Vanuatu to understand how new structures and processes become adopted at scale. A theory of scaling for CBFM guides the analysis of regime shifts over time.

In vitro mannosidase activity of EDEM3 against asparagine-linked oligomannose-type glycans.

Oligomannose-type glycans on glycoproteins play an important role in the endoplasmic reticulum (ER)-protein quality control. Mannose trimming of the glycans triggers the ER-associated protein degradation pathway. In mammals, ER mannosyl-oligosaccharide 1,2-α-mannosidase 1 and three ER degradation -enhancing α-mannosidase-like proteins (EDEMs) are responsible for mannose trimming.

Combination of recommender system and single-particle diagnosis for accelerated discovery of novel nitrides.

Discovery of new compounds from wide chemical space is attractive for materials researchers. However, theoretical prediction and validation experiments have not been systematically integrated. Here, we demonstrate that a new combined approach is powerful in significantly accelerating the discovery rate of new compounds, which should be useful for exploration of a wide chemical space in general.

Dimerization of ER-resident molecular chaperones mediated by ERp29.

The lectin chaperones calnexin (CNX) and calreticulin (CRT) localized in the endoplasmic reticulum play important roles in glycoprotein quality control. Although the interaction between these lectin chaperones and ERp57 is well known, it has been recently reported that endoplasmic reticulum protein 29 (ERp29), a member of PDI family, interacts with CNX and CRT. The biochemical function of ERp29 is unclear because it exhibits no ERp57-like redox activity.

Glycan dependent refolding activity of ER glucosyltransferase (UGGT).

Background: In the endoplasmic reticulum (ER), folding of glycoproteins is assisted by a combined action of enzymes and chaperones that leads them to biologically functional structures. In this system, UDP-glucose:glycoprotein glucosyltransferase 1 (UGGT1) plays an essential role as the "folding sensor" by virtue of its ability to discriminate folding states of client glycoproteins. However, besides its transferase activity, whether UGGT1 possesses any chaperone activity that facilitates protein folding is yet to be addressed.

Compositional descriptor-based recommender system for the materials discovery.

Structures and properties of many inorganic compounds have been collected historically. However, it only covers a very small portion of possible inorganic crystals, which implies the presence of numerous currently unknown compounds. A powerful machine-learning strategy is mandatory to discover new inorganic compounds from all chemical combinations.

Linearized machine-learning interatomic potentials for non-magnetic elemental metals: Limitation of pairwise descriptors and trend of predictive power.

Machine-learning interatomic potential (MLIP) has been of growing interest as a useful method to describe the energetics of systems of interest. In the present study, we examine the accuracy of linearized pairwise MLIPs and angular-dependent MLIPs for 31 elemental metals. Using all of the optimal MLIPs for 31 elemental metals, we show the robustness of the linearized frameworks, the general trend of the predictive power of MLIPs, and the limitation of pairwise MLIPs.

Substrate Recognition of Glycoprotein Folding Sensor UGGT Analyzed by Site-Specifically N-Labeled Glycopeptide and Small Glycopeptide Library Prepared by Parallel Native Chemical Ligation.

UDP-glucose:glycoprotein glucosyltransferase (UGGT) distinguishes glycoproteins in non-native conformations from those in native conformations and glucosylates from only non-native glycoproteins. To analyze how UGGT recognizes non-native glycoproteins, we chemically synthesized site-specifically N-labeled interleukin 8 (IL-8) C-terminal (34-72) glycopeptides bearing a ManGlcNAc (M9) oligosaccharide. Chemical shift perturbation mapping NMR experiments suggested that Phe65 of the glycopeptide specifically interacts with UGGT.

PDI family protein ERp29 recognizes P-domain of molecular chaperone calnexin.

Endoplasmic reticulum (ER) resident lectin chaperone calnexin (CNX) and calreticulin (CRT) assist folding of nascent glycoproteins. Their association with ERp57, a member of PDI family proteins (PDIs) which promote disulfide bond formation of unfolded proteins, has been well documented. Recent studies have provided evidence that other PDIs may also interact with CNX and CRT.

Endo-α-Mannosidase-Catalyzed Transglycosylation.

In order for facilitating the synthesis of oligosaccharides, transglycosylation reactions mediated by glycoside hydrolases have been studied in various contexts. In this study, we examined the transglycosylating activity of a Golgi endo-α-mannosidase. We prepared various glycosyl donors and acceptors, and recombinant human Golgi endo-α-mannosidase and its various mutants were expressed.

Non-enzymatic reaction of glycosyl oxazoline with peptides.

Recently, a number of chemoenzymatic strategies have been explored for achieving preparation of homogeneous glycopeptides and glycoproteins, especially by using endoglycanases and glycosyl oxazolines. However, concomitant occurrence of non-enzymatic reactions has been reported, but no further characterization of the byproducts was conducted. In this work, we made an attempt to identify the side product by using model substrates.

Direct assay for endo-α-mannosidase substrate preference on correctly folded and misfolded model glycoproteins.

We previously reported a unique assay system for UDP-glucose glycoprotein glucosyltransferase (UGGT) toward glycoprotein folding intermediates during the folding process. The assay involved the in vitro folding of both high-mannose type oligosaccharyl crambin, which yielded only the correctly folded glycoprotein form (M9-glycosyl-native-crambin), and its mutant, which yielded misfolded glycoproteins (M9-glycosyl-misfolded-crambin), in the presence of UGGT. The process successfully yielded both mono-glucosylated M9-glycosyl-native-crambin (G1M9-glycosyl-native-crambin) and M9-glycosyl-misfolded-crambin (G1M9-glycosyl-misfolded-crambin).

Effects of domain composition on catalytic activity of human UDP-glucose:glycoprotein glucosyltransferases.

Uridine diphosphate (UDP)-glucose:glycoprotein glucosyltransferase (UGGT) 1 is a soluble protein residing in the endoplasmic reticulum (ER) and partially in ER-Golgi intermediate compartment. Characteristically, it is able to recognize incompletely folded proteins and re-glucosylate their high-mannose-type glycans. By virtue of this, UGGT1 acts as a folding sensor in the glycoprotein quality control system in the ER.

Synthesis of misfolded glycoprotein dimers through native chemical ligation of a dimeric peptide thioester.

Glycoprotein quality control processes are very important for an efficient production of glycoproteins and for avoiding the accumulation of unwanted toxic species in cells. These complex processes consist of multiple enzymes and chaperones such as UGGT, calnexin/calreticulin, and glucosidase II. We designed and synthesized monomeric and dimeric misfolded glycoprotein probes.

Structural Analysis of Free N-Glycans in α-Glucosidase Mutants of Saccharomyces cerevisiae: Lack of the Evidence for the Occurrence of Catabolic α-Glucosidase Acting on the N-Glycans.

Saccharomyces cerevisiae produces two different α-glucosidases, Glucosidase 1 (Gls1) and Glucosidase 2 (Gls2), which are responsible for the removal of the glucose molecules from N-glycans (Glc3Man9GlcNAc2) of glycoproteins in the endoplasmic reticulum. Whether any additional α-glucosidases playing a role in catabolizing the glucosylated N-glycans are produced by this yeast, however, remains unknown. We report herein on a search for additional α-glucosidases in S.

Synthesis of Glc1Man9-Glycoprotein Probes by a Misfolding/Enzymatic Glucosylation/Misfolding Sequence.

Glycoproteins in non-native conformations are often toxic to cells and may cause diseases, thus the quality control (QC) system eliminates these unwanted species. Lectin chaperone calreticulin and glucosidase II, both of which recognize the Glc1 Man9 oligosaccharide on glycoproteins, are important components of the glycoprotein QC system. Reported herein is the preparation of Glc1 Man9 -glycoproteins in both native and non-native conformations by using the following sequence: misfolding of chemically synthesized Man9 -glycoprotein, enzymatic glucosylation, and another misfolding step.

Endoplasmic Reticulum (ER)-Targeted, Galectin-Mediated Retrograde Transport by Using a HaloTag Carrier Protein.

Investigations into metabolic processes within the cell have often relied on genetic methods such as forced expression and knockout or knockdown techniques. An alternative approach would be introducing a molecule into the desired location inside the cell. To translocate compounds from outside cells into the endoplasmic reticulum (ER), we constructed a delivery carrier protein.

Hydrophobic Tagged Dihydrofolate Reductase for Creating Misfolded Glycoprotein Mimetics.

In the endoplasmic reticulum (ER), nascent glycoproteins that have not acquired the native conformation are either repaired or sorted for degradation by specific quality-control systems composed by various proteins. Among them, UDP-glucose:glycoprotein glucosyltransferase (UGGT) serves as a folding sensor in the ER. However, the molecular mechanism of its recognition remains obscure.

Prediction of Low-Thermal-Conductivity Compounds with First-Principles Anharmonic Lattice-Dynamics Calculations and Bayesian Optimization.

Compounds of low lattice thermal conductivity (LTC) are essential for seeking thermoelectric materials with high conversion efficiency. Some strategies have been used to decrease LTC. However, such trials have yielded successes only within a limited exploration space.