Characterization of amino acid ligases and development of production processes for peptide containing D-amino acid

制度:新 ; 文部省報告番号:甲2399号 ; 学位の種類:博士(工学) ; 授与年月日:2007/3/15 ; 早大学位記番号:新448

Allosteric Regulation of HIV-1 Reverse Transcriptase by ATP for Nucleotide Selection

Background: Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is a DNA polymerase that converts viral RNA genomes into proviral DNAs. How HIV-1 RT regulates nucleotide selectivity is a central issue for genetics and the nucleoside analog RT inhibitor (NRTI) resistance of HIV-1. Methodology/Principal Findings: Here we show that an ATP molecule at physiological concentrations acts as an allosteric regulator of HIV-1 RT to decrease the Km value of the substrate, decrease the kcat value, and increase the Ki value of NRTIs for RT. Computer-assisted structural analyses and mutagenesis studies suggested the positions of the ATP molecule and NRTIresistance mutations during a catalytic reaction, which immediately predict possible influences on nucleotide insertion into the catalytic site, the DNA polymerization, and the excision reaction. Conclusions/Significance: These data imply that the ATP molecule and NRTI mutations can modulate nucleotide selectivity by altering the fidelity of the geometric selection of nucleotides and the probability of an excision reaction

Drum Beating and a Martial Art Bojutsu Performed by a Humanoid Robot

Over the past few decades a considerable number of studies have been made on impact dynamics. Zheng and Hemami discussed a mathematical model of a robot that collides with an environment (Zheng & Hemami, 1985). When a robot arm fixed on the ground collides with a hard environment, the transition from the free space to constrained space may bring instabilit

Bayesian Approach to Find a Long-Term Trend in Erratic Polarization Variations Observed in Blazars

We developed a method to separate a long-term trend from observed temporal variations of polarization in blazars using a Bayesian approach. The temporal variation of the polarization vector is apparently erratic in most blazars, while several objects occasionally exhibited systematic variations, for example, an increase of the polarization degree associated with a flare of the total flux. We assume that the observed polarization vector is a superposition of distinct two components, a long-term trend and a short-term variation component responsible for short flares. Our Bayesian model estimates the long-term trend which satisfies the condition that the total flux correlates with the polarized flux of the short-term component. We demonstrate that assumed long-term polarization components are successfully separated by the Bayesian model for artificial data. We applied this method to photopolarimetric data of OJ 287, S5 0716+714, and S2 0109+224. Simple and systematic long-term trends were obtained in OJ 287 and S2 0109+224, while no such a trend was identified in S5 0716+714. We propose that the apparently erratic variations of polarization in OJ 287 and S2 0109+224 are due to the presence of the long-term polarization component. The behavior of polarization in S5 0716+714 during our observation period implies the presence of a number of polarization components having a quite short time-scale of variations.Comment: 12 pages, 7 figures, accepted for publication in PAS

SL1 revisited: functional analysis of the structure and conformation of HIV-1 genome RNA

Additional file 1: Figure S1. Native northern blots of HIV-1 genome RNA in virion. Figure S2. The schema of the system for estimating HIV-1 recombination efficiency