Assessing Computational Amino Acid β-Turn Propensities with a Phage-Displayed Combinatorial Library and Directed Evolution

SummaryStructure propensities of amino acids are important determinants in guiding proteins' local and global structure formation. We constructed a phage display library—a hexa-HIS tag upstream of a CXXC (X stands for any of the 20 natural amino acids) motif appending N-terminal to the minor capsid protein pIII of M13KE filamentous phage—and developed a novel directed-evolution procedure to select for amino acid sequences forming increasingly stable β-turns in the disulfide-bridged CXXC motif. The sequences that emerged from the directed-evolution cycles were in good agreement with type II β-turn propensities derived from surveys of known protein structures, in particular, Pro-Gly forming a type II β-turn. The agreement strongly supported the notion that β-turn formation plays an active role in initiating local structure folding in proteins

Endoscopic Balloon Dilatation for Esophageal Strictures in Children Younger Than 6 Years: Experience in a Medical Center

Esophageal strictures in children may be caused by congenital anomaly, caustic agent or foreign body ingestion, complication of reflux esophagitis, and after esophageal surgery. Accidental ingestion of alkaline fluid is the most common cause of corrosive esophagitis in children in Taiwan. In this article, we studied 10 pediatric patients who had esophageal strictures and required endoscopic balloon dilatation (EBD) therapy under general anesthesia from January 2003 to June 2009. The median age of the studied children who received their first EBD treatment was 36.2 months (13.4–60.9 months), with a dilator size of 8.0mm (5–12 mm). The interval between injury and initial EBD was 3.0 months (1.3–60.8 months). The treatment duration averaged 16.7 months (3.0–69.3 months), with 13.5 (4–31) instances of EBD therapy per patient. The greater the length of stricture, the more number of times EBD was needed. In these cases, no severe complication was found after the procedure. The result indicated that EBD under general anesthesia was a safe and effective method to resolve the symptom of dysphagia and diet condition. Because of the limited number of study cases, long-term studies are required to further confirm the clinical effect of EBD under general anesthesia

YamSat: the First Picosatellite being Developed in Taiwan

This paper describes the current planning and design of the YamSat, the first picosatellite being developed in Taiwan. The design, analysis, manufacture, integration, test and operation of the YamSat will be performed by the National Space Program Office (NSPO), Taiwan, R.O.C, in cooperation with other domestic organizations and companies. It is a member of the CubeSat [1], 10cm x 10cm x 10cm size and within 1kg mass. The major objective of the YamSat is to qualify in space the components and technology developed in Taiwan, including a micro-spectrometer payload using Micro Electro Mechanical Systems (MEMS) technology. The YamSat will be ready for flight in the middle of 2002

Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface

Protein-protein interactions are critical determinants in biological systems. Engineered proteins binding to specific areas on protein surfaces could lead to therapeutics or diagnostics for treating diseases in humans. But designing epitope-specific protein-protein interactions with computational atomistic interaction free energy remains a difficult challenge. Here we show that, with the antibody-VEGF (vascular endothelial growth factor) interaction as a model system, the experimentally observed amino acid preferences in the antibody-antigen interface can be rationalized with 3-dimensional distributions of interacting atoms derived from the database of protein structures. Machine learning models established on the rationalization can be generalized to design amino acid preferences in antibody-antigen interfaces, for which the experimental validations are tractable with current high throughput synthetic antibody display technologies. Leave-one-out cross validation on the benchmark system yielded the accuracy, precision, recall (sensitivity) and specificity of the overall binary predictions to be 0.69, 0.45, 0.63, and 0.71 respectively, and the overall Matthews correlation coefficient of the 20 amino acid types in the 24 interface CDR positions was 0.312. The structure-based computational antibody design methodology was further tested with other antibodies binding to VEGF. The results indicate that the methodology could provide alternatives to the current antibody technologies based on animal immune systems in engineering therapeutic and diagnostic antibodies against predetermined antigen epitopes

ITPKC Single Nucleotide Polymorphism Associated with the Kawasaki Disease in a Taiwanese Population

Kawasaki disease (KD) is characterized by systemic vasculitis with unknown etiology. Previous studies from Japan indicated that a gene polymorphism of ITPKC (rs28493229) is responsible for susceptibility to KD. We collected DNA samples from 1,531 Taiwanese subjects (341 KD patients and 1,190 controls) for genotyping ITPKC. In this study, no significant association was noted for the ITPKC polymorphism (rs28493229) between the controls and KD patients, although the CC genotype was overrepresented. We further combined our data with previously published case/control KD studies in the Taiwanese population and performed a meta-analysis. A significant association between rs28493229 and KD was found (Odds Ratio:1.36, 95% Confidence Interval 1.12–1.66). Importantly, a significant association was obtained between rs28493229 and KD patients with aneurysm formation (P = 0.001, under the recessive model). Taken together, our results indicated that C-allele of ITPKC SNP rs28493229 is associated with the susceptibility and aneurysm formation in KD patients in a Taiwanese population

Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with the physicochemical complementarity features based on the non-covalent interaction data derived from protein interiors

Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors

The site on the HIV-1 gp120 glycoprotein that binds the CD4 receptor is recognized by broadly reactive antibodies, several of which neutralize over 90% of HIV-1 strains. To understand how antibodies achieve such neutralization, we isolated CD4-binding-site (CD4bs) antibodies and analyzed 16 co-crystal structures –8 determined here– of CD4bs antibodies from 14 donors. The 16 antibodies segregated by recognition mode and developmental ontogeny into two types: CDR H3-dominated and VH-gene-restricted. Both could achieve greater than 80% neutralization breadth, and both could develop in the same donor. Although paratope chemistries differed, all 16 gp120-CD4bs antibody complexes showed geometric similarity, with antibody-neutralization breadth correlating with antibody-angle of approach relative to the most effective antibody of each type. The repertoire for effective recognition of the CD4 supersite thus comprises antibodies with distinct paratopes arrayed about two optimal geometric orientations, one achieved by CDR H3 ontogenies and the other achieved by VH-gene-restricted ontogenies

External-forcing modulation on temporal variations of hydrothermalism-evidence from sediment cores in a submarine venting field off northeastern Taiwan.

The temporal variation of sulfur and metals in core sediments off Kueishantao Islet, a hydrothermal vent site at northeastern Taiwan, was explored to elucidate the changes in submarine hydrothermal emanation over a centennial time scale. The discharge of acidic fluids containing abundant sulfides and dissolved metals results in different concentrations of sulfur and metal accumulating in deposited sediments. In addition to particle size and organic carbon affecting metal contents, the content of total sulfur (TS), which is regarded as an indicator of hydrothermalism, correlates positively and strongly with Fe and other metals; however, it correlates negatively with another index of hydrothermalism, the Al/(Al+Fe+Mn) ratio. The TS content in Core Ks2, the core closest to the vents, increased during 1950-1956, 1968-1970, 1982-1987, 1990-1992, and 2004-2005, but decreased during 1967-1968, 1988-1990, and 1994-1995. The chronological changes in the TS concentration of Cores Ks3 and S2 were very similar to those of Core Ks2 within the aforementioned time spans. The numerous large earthquakes (ML > 5) and typhoons that affect northeastern Taiwan appear to influence hydrothermal emanation and determine the temporal variation of sulfur and metals in sediment cores

Lived experience of patients undergoing allogeneic peripheral hematopoietic stem cell transplant

[[abstract]]Hematopoietic stem cell transplantation offers cancer patients hope for a cure. However, during the transplant process, patients experience great discomfort, which has a sustantial impact on their psychological, social, and spiritual well-being and severely affects their quality of life. The objective of this study was to understand the lived experience of patients during the period from 100 days to 1 year after undergoing an allogeneic peripheral hematopoietic stem cell transplant. A phenomenological method proposed by Giorgi, purposive sampling, and in-depth interviews were used. We interviewed 14 patients (9 males, 5 females) in the hematology and oncology outpatient department of a teaching hospital in central Taiwan. Analysis of the interviews revealed 6 themes: interference of symptoms, interruption of important developmental tasks, low self-value, unbreakable shackles, support network, and living in the moment. Although the physical, psychological, and social functions of the participants gradually stabilized during the year after their transplant, several symptoms continued to interfere with their daily lives. They doubted their ability to contribute to their family, worried about their competence to have children, and faced threats of graft rejection, cancer recurrence, and even death. However, by leaning on social supports, thinking positively, and maintaining hope, participants were eventually able to return to normal lives and plan for the future. Health professionals should actively provide transplant patients with relevant information and should assist patients in alleviating physical and psychological pain and in maintaining social contacts and hop