ProteoFind : A script for finding proteins that are suitable for chemical synthesis

ProteoFind is a computational script for finding proteins that are suitable for fragment ligation-based chemical synthesis. This paper describes the development and case studies of ProteoFind, which searches protein lists obtained from the UniProt website. Its application to visualize areas covered by several one-pot three-fragment ligation methods is also discussed. The results demonstrate that ProteoFind not only saves time when searching for synthetic target proteins, but also proposes many candidate proteins from among which biomedically interesting proteins could be found. It also enables clarification of the features of ligation methods by comparing the areas to which each ligation reaction is accessible

Collisional bending of the western Paleo-Kuril Arc deduced from paleomagnetic analysis and U–Pb age determination

The Paleo‐Kuril Arc in the eastern Hokkaido region of Japan, the westernmost part of the Kuril Arc in the northwestern Pacific region, shows a tectonic bent structure. This has been interpreted, using paleomagnetic data, to be the result of block rotations in the Paleo‐Kuril Arc. To understand the timing and origin of this tectonic bent structure in the Paleo‐Kuril arc‐trench system, paleomagnetic surveys and U–Pb radiometric dating were conducted in the Paleogene Urahoro Group, which is distributed in the Shiranuka‐hill region, eastern Hokkaido. The U–Pb radiometric dating indicated that the Urahoro Group was deposited at approximately 39 Ma. Paleomagnetic analysis of the Urahoro Group suggested that the Shiranuka‐hill region experienced a 28° clockwise rotation with respect to East Asia. The degree of clockwise rotation implied from the Urahoro Group is smaller than that of the underlying Lower Eocene Nemuro Group (62°) but larger than that of the overlying Onbetsu Group (−9°). It is thus suggested that the Shiranuka‐hill region experienced a clockwise rotation of approximately 34° between the deposition of the Nemuro and Urahoro Groups (50–39 Ma), and a 38° clockwise rotation between the deposition of the Urahoro and Onbetsu Groups (39–34 Ma). The origin of the curved tectonic belt of the Paleo‐Kuril Arc was previously explained by the opening of the Kuril Basin after 34 Ma. The age constraint for the rotational motion of the Shiranuka‐hill region in this study contradicts this hypothesis. Consequently, it is suggested that the process of arc–arc collision induced the bent structure of the western Paleo‐Kuril Arc

Resin-Bound Crypto-Thioester for Native Chemical Ligation

Resin-bound N–sulfanylethylanilide (SEAlide) peptide was found to function as a crypto-thioester peptide. Exposure of the peptide resin to an aqueous solution under neutral conditions in the presence of thiols affords thioesters without accompanying racemization of C-terminal amino acids. Furthermore, the resin-bound SEAlide peptides react with N-terminal cysteinyl peptides in the absence of phosphate salts to afford ligated products, whereas soluble SEAlide peptides do not. This unexpected difference in reactivity of the SEAlide peptides allows for a one-pot/three-fragment ligation using resin-bound and unbound peptides

Deprotection of S-Acetamidomethyl Cysteine with Copper (II) and 1,2-Aminothiols under Aerobic Conditions

Ring-opening by CuSO4 of a 1,3-thiazolidine carbonyl structure (Thz) as an N-terminal cysteine (Cys) residue revealed that an intramolecular S–acetamidomethyl cysteine (Cys(Acm)) can also be deprotected with concomitant formation of a disulphide bond connecting the two Cys residues. A mechanistic study on the disulphide formation led to a general protocol for deprotection of the S-Acm group by CuSO4 and a 1,2-aminothiol under aerobic conditions. Application of this new deprotection reaction allowed for the synthesis of Apamin, a peptide with two-disulphides in a one-pot/stepwise disulphide-bridging procedure

CXCL14 Acts as a Specific Carrier of CpG DNA into Dendritic Cells and Activates Toll-like Receptor 9-mediated Adaptive Immunity

CXCL14 is a primordial chemokine that plays multiple roles in tumor suppression, autoimmune arthritis, and obesity-associated insulin resistance. However, the underlying molecular mechanisms are unclear. Here, we show that CXCL14 transports various types of CpG oligodeoxynucleotide (ODN) into the endosomes and lysosomes of bone marrow-derived dendritic cells (DCs), thereby activating Toll-like receptor 9 (TLR9). A combination of CpG ODN (ODN2395) plus CXCL14 induced robust production of IL-12 p40 by wild-type, but not Tlr9-knockout, DCs. Consistent with this, ODN2395-mediated activation of DCs was significantly attenuated in Cxcl14-knockout mice. CXCL14 bound CpG ODN with high affinity at pH 7.5, but not at pH 6.0, thereby enabling efficient delivery of CpG ODN to TLR9 in the endosome/lysosome. Furthermore, the CXCL14-CpG ODN complex specifically bound to high affinity CXCL14 receptors on DCs. Thus, CXCL14 serves as a specific carrier of CpG DNA to sensitize TLR9-mediated immunosurveillance

Randomized Controlled Trial of Two Forms of Self-Management Group Education in Japanese People with Impaired Glucose Tolerance

The aim of this study was to determine the effectiveness of education on diabetes prevention in subjects with impaired glucose tolerance. A total of 100 subjects of impaired glucose tolerance with hemoglobin A1c (HbA1c) levels ≥5.5 to <6.1% were assigned randomly to either support or control groups. All subjects received education in 8 sessions over a 6-month period. The support group consisted of 10 members collaborating with a dietitian or a nurse who learned coping skills by employing a participant-centered approach. Participants in the support group were required to keep a diary that monitored weight, food intake and blood glucose levels, while the control group attended several lectures. Subjects assigned to the support group had a reduction in mean HbA1c levels from 5.77 ± 0.36% at baseline to 5.39 ± 0.24% at the endpoint (p<0.01). Weight, total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels also decreased (p<0.01) in the support group, whereas subjects in the control group had no observable reduction in these indices. After intervention, participants of the support group had improvements in their 2-h post-meal blood glucose levels. Support group education can be effective for improving glycemic control in participants when carried out in collaboration with educators and other team members

Facile synthesis of C-terminal peptide thioacids under mild conditions from N-sulfanylethylanilide peptides

A facile procedure has been developed for the synthesis of C-terminal peptide thioacids under mild conditions. A series of N-sulfanylethylanilide peptides prepared using Fmoc-based solid-phase peptide synthesis were successfully converted to the corresponding thioacids via a hydrothiolysis reaction in a phosphate buffer with only trace epimerization of the C-terminal amino acid

Development of an anilide-type scaffold for the thioester precursor, N-Sulfanylethylcoumarinyl amide (SECmide)

N-Sulfanylethylcoumarinyl amide (SECmide) peptide, which was initially developed for the use in the fluorescence-guided detection of promoters of N–S acyl transfer, was successfully applied to a facile and side reaction-free protocol for N–S acyl-transfer-mediated synthesis of peptide thioesters. Additionally, 4-mercapto benzyl phosphonic acid (MBPA) was proved to be a useful catalyst for the SECmide or N-sulfanylethylanilide (SEAlide)-mediated NCL reaction

Tailored Synthesis of 162-Residue S-Monoglycosylated GM2-Activator Protein (GM2AP) Analogues that Allows Facile Access to Protein Library

A synthetic protocol has been developed for the preparation of 162-residue S-monoglycosylated GM2-activator protein (GM2AP) analogues bearing various amino acid substitutions for Thr69. The facile incorporation of the replacements into the protein was achieved by a one-pot/N–to–C-directed sequential ligation strategy using readily accessible middle N-sulfanylethylanilide (SEAlide) peptides consisting of seven amino acid residues. A kinetically-controlled ligation protocol was successfully applied to the assembly of three peptide segments covering the GM2AP. The native chemical ligation (NCL) reactivities of the SEAlide can be tuned by the presence or absence of phosphate salts. Furthermore, the NCL of the alkyl thioester fragment (GM2AP (1–31)) with the N-terminal cysteinyl prolyl thioester (GM2AP (32–67)) proceeded smoothly to yield the 67-residue prolyl thioester, with the prolyl thioester moiety remaining intact. This newly developed strategy enabled the facile synthesis of GM2AP analogues. Thus, we refered this synthetic protocol as “Tailored Synthesis” for the construction of a GM2AP library