Prediction of protein motions from amino acid sequence and its application to protein-protein interaction

BACKGROUND: Structural flexibility is an important characteristic of proteins because it is often associated with their function. The movement of a polypeptide segment in a protein can be broken down into two types of motions: internal and external ones. The former is deformation of the segment itself, but the latter involves only rotational and translational motions as a rigid body. Normal Model Analysis (NMA) can derive these two motions, but its application remains limited because it necessitates the gathering of complete structural information. RESULTS: In this work, we present a novel method for predicting two kinds of protein motions in ordered structures. The prediction uses only information from the amino acid sequence. We prepared a dataset of the internal and external motions of segments in many proteins by application of NMA. Subsequently, we analyzed the relation between thermal motion assessed from X-ray crystallographic B-factor and internal/external motions calculated by NMA. Results show that attributes of amino acids related to the internal motion have different features from those related to the B-factors, although those related to the external motion are correlated strongly with the B-factors. Next, we developed a method to predict internal and external motions from amino acid sequences based on the Random Forest algorithm. The proposed method uses information associated with adjacent amino acid residues and secondary structures predicted from the amino acid sequence. The proposed method exhibited moderate correlation between predicted internal and external motions with those calculated by NMA. It has the highest prediction accuracy compared to a naïve model and three published predictors. CONCLUSIONS: Finally, we applied the proposed method predicting the internal motion to a set of 20 proteins that undergo large conformational change upon protein-protein interaction. Results show significant overlaps between the predicted high internal motion regions and the observed conformational change regions

Storing Medical Records of A-Bomb Survivors on Optical Disks

Medical records of A-bomb survivors include numerical data and non-numerical data such as handwritten description. We have been storing the numerical data in medical records into a data base. We started to store the nonnumerical data on optical disks. We analyzed the significance and usefulness of storing them. The nonnumerical data of symptoms can not be evaluated by but can be analyzed with the numerical data. It was concluded that storing non-numerical data in the medical records on the optical disks would be worthy

Effect of Intravenous Immunostimulant (OK-432)

To clarify the effectiveness of OK-432, immunopotentiator was intravenously used. The tumor-bearing host was apparently stimulated via NK activity and increased the number of T cells and B cells. It helps immunodepressed host to level up quickly. However, further effective immunostimulation beyond the normal range could not be expected. A new combined method should be found to be immunopotentiated even for the uncompromized host. Recently, a new immunostimulant derived from streptococcus, OK-432, was widely used for the treatment of cancer in Japan. The cytostatic and cytotoxic actions of OK-432 for cancer cells have been made clear by in vitro and vivo study. It, however, is not clear as to how the developing immunostimulated states differ on the condition of admistering route, dosis or time-intlrval. In this series, the effects of intravenous administration of OK-432 as the host immunostimulator were compared with those of conventional subcutaneous administration

Factors Determining Satisfaction with Daily Life of Elderly A-bomb Survivors

From the analysis of questionnaires to elderly A-bomb survivors of over 65 years old, we analysed factors which determined satisfaction with daily life. Analysed categories were housing condition, life style, occupational status, health condition and family status. From the analysis, to be an A-bomb survivor was not a factor for satisfaction with daily life, and it became clear that living in a rented room, not satisfying one\u27s job and low income were serious factors which kept elderly people from the satisfaction with daily life. It must be necessary to improve these factors for the satisfaction of elderly people

Estimation of Spin-Spin Interaction by Weak Measurement Scheme

Precisely knowing an interaction Hamiltonian is crucial to realize quantum information tasks, especially to experimentally demonstrate a quantum computer and a quantum memory. We propose a scheme to experimentally evaluate the spin-spin interaction for a two-qubit system by the weak measurement technique initiated by Yakir Aharonov and his colleagues. Furthermore, we numerically confirm our proposed scheme in a specific system of a nitrogen vacancy center in diamond. This means that the weak measurement can also be taken as a concrete example of the quantum process tomography.Comment: 4 pages, 1 table, 2 figures, to appear in Europhysics Letter

Weak measurement of photon polarization by back-action induced path interference

The essential feature of weak measurements on quantum systems is the reduction of measurement back-action to negligible levels. To observe the non-classical features of weak measurements, it is therefore more important to avoid additional back-action errors than it is to avoid errors in the actual measurement outcome. In this paper, it is shown how an optical weak measurement of diagonal (PM) polarization can be realized by path interference between the horizontal (H) and vertical (V) polarization components of the input beam. The measurement strength can then be controlled by rotating the H and V polarizations towards each other. This well-controlled operation effectively generates the back-action without additional decoherence, while the visibility of the interference between the two beams only limits the measurement resolution. As the experimental results confirm, we can obtain extremely high weak values, even at rather low visibilities. Our method therefore provides a realization of weak measurements that is extremely robust against experimental imperfections.Comment: 11 pages, 3 figure

Weak Values with Decoherence

The weak value of an observable is experimentally accessible by weak measurements as theoretically analyzed by Aharonov et al. and recently experimentally demonstrated. We introduce a weak operator associated with the weak values and give a general framework of quantum operations to the W operator in parallel with the Kraus representation of the completely positive map for the density operator. The decoherence effect is also investigated in terms of the weak measurement by a shift of a probe wave function of continuous variable. As an application, we demonstrate how the geometric phase is affected by the bit flip noise.Comment: 17 pages, 3 figure