Docking dynamics and electronic structure of metalloprotein complexes

取得学位：博士(理学)，学位授与番号：博甲第860号，学位授与年月日：平成19年3月22

A method of classification and recognition of blue copper protein

金沢大学大学院自然科学研究科計算科学金沢大学理学部Some proteins in blue copper proteins have similar properties. In some cases it is not easy to distinguish the proteins each other. The study to recognize and classify in blue copper proteins has important roles to recognize the difference of similar properties, for examples, structures and residue sequences in blue copper proteins. There are many methods being developed to predict protein structure from many approachs, which one still not satisfactory yet. Therefore it is a challenge for scientists to develop or improve their methods. One of promising method is artificial neural networks (ANN). ANN is learning machine methods consisted of input, hidden and output layer. ANN is tested to recognize secondary structure in blue copper protein. It is found that ANN can distinguish for 7-type of secondary structure and recognize 72% secondary structure in blue copper protein. © 2006 American Institute of Physics

Binding free energy calculation and structural analysis for antigen-antibody complex

金沢大学大学院自然科学研究科計算科学金沢大学理学部Recently, much attention has been directed to calculational prediction for binding free energy and structural analysis for biomolecule complex in solvate state. We investigated Influenza Hemagglutinin (wild type HA), mutated HA and its neutralize antibody Fab fragment complex in explicit solvent water molecules by molecular dynamics simulation(MD). B-factor and binding free energy of loop structures in the complex structure are calculated. The calculation result supports the experimental result in a qualitative tendency. MD calculation also shows that hydrogen bond distance differs between wild type HA and mutated HA, which contributes to the difference of binding free energy and structural stability. These result suggests that pattern of making hydrogen bonds in crystal structure are almost kept even in solvate state. © 2006 American Institute of Physics

Three Japanese patients with congenital pituitary hormone deficiency and ophthalmological anomalies

The clinical phenotype of congenital pituitary hormone deficiency is variable and can be associated with a number of structural abnormalities of the central nervous system. We report three Japanese patients with congenital pituitary hormone deficiency and ophthalmological anomalies. Two of the patients initially showed strabismus and unilateral optic nerve hypoplasia. Thereafter, growth failure became evident, leading to the diagnosis of pituitary hormone deficiency. The other patient had severe congenital hypopituitarism with respiratory distress and hypoglycemia from the first day of life. In addition, he had prolonged jaundice and impaired liver function with bilateral optic nerve hypoplasia. Neuroimaging of the pituitary region in all three patients demonstrated a small anterior pituitary lobe and no pituitary stalk. Our findings indicate that clinical variability of congenital hypopituitarism must be considered. In a patient with ophthalmological symptoms, endocrine evaluation and neuroimaging of the CNS including the pituitary region should be considered

Molecular dynamics study of hydration water behavior in blue copper protein

金沢大学大学院自然科学研究科計算科学金沢大学理学部We carry out the molecular dynamics(MD) simulation of type 1 blue copper protein azurin in room and some lower temperatures to investigate the behavior of hydration water molecules in the protein surface. In this study, we find the anomalous behavior of the water molecules, which depend on the system temperatures. These water molecules have hydrogen bond to the protein surface residues. We specify the residues type, being classified as the hydration donor and the hydration acceptor of water molecules. We analyze the residue type, and the bond length and bond strength between solvent water molecules in each temperature. Moreover, we estimate the B-factor of these residues which indicates the fluctuation of hydration residues in each temperature. B-factor values depend on the system temperatue althought the number of hydration residue do not depend on the temperature. © 2006 American Institute of Physics

Solvent effects on electronic structure of active site of azurin by polarizable continuum model

We present a cluster model for the active site of oxidized azurin, and investigate the electronic structure of the active site of oxidized azurin by using density functional calculations with polarizable continuum model. The singly occupied molecular orbital and spin density in the model widely distribute around the Cu 3dx2-y2 and S(Cys112) 3p orbitals. The dependency of electronic properties such as partial charge density and spin density on the dielectric constant is discussed. We find that partial spin density and charge density on the copper ion become larger, when the dielectric constant increases. © 2005 Elsevier Ltd. All rights reserved.Embargo Period 24 month

Alternative splicing produces structural and functional changes in CUGBP2

<p>Abstract</p> <p>Background</p> <p>CELF/Bruno-like proteins play multiple roles, including the regulation of alternative splicing and translation. These RNA-binding proteins contain two RNA recognition motif (RRM) domains at the N-terminus and another RRM at the C-terminus. CUGBP2 is a member of this family of proteins that possesses several alternatively spliced exons.</p> <p>Results</p> <p>The present study investigated the expression of exon 14, which is an alternatively spliced exon and encodes the first half of the third RRM of CUGBP2. The ratio of exon 14 skipping product (<it>R3δ</it>) to its inclusion was reduced in neuronal cells induced from P19 cells and in the brain. Although full length CUGBP2 and the CUGBP2 <it>R3δ </it>isoforms showed a similar effect on the inclusion of the smooth muscle (SM) exon of the <it>ACTN1 </it>gene, these isoforms showed an opposite effect on the skipping of exon 11 in the <it>insulin receptor </it>gene. In addition, examination of structural changes in these isoforms by molecular dynamics simulation and NMR spectrometry suggested that the third RRM of R3δ isoform was flexible and did not form an RRM structure.</p> <p>Conclusion</p> <p>Our results suggest that CUGBP2 regulates the splicing of <it>ACTN1 </it>and <it>insulin receptor </it>by different mechanisms. Alternative splicing of <it>CUGBP2 </it>exon 14 contributes to the regulation of the splicing of the <it>insulin receptor</it>. The present findings specifically show how alternative splicing events that result in three-dimensional structural changes in CUGBP2 can lead to changes in its biological activity.</p